Glycoprotein synthesis

ABSTRACT

Methods for making glycoproteins, both in vitro and in vivo, are provided. One method involves incorporating an unnatural amino acid into a protein and attaching one or more saccharide moieties to the unnatural amino acid. Another method involves incorporating an unnatural amino acid that includes a saccharide moiety into a protein. Proteins made by both methods can be further modified with additional sugars.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to and benefit of U.S. provisionalpatent application Ser. No. 60/419,265, filed Oct. 16, 2002, U.S.provisional patent application Ser. No. 60/420,990, filed Oct. 23, 2002,and U.S. provisional patent application Ser. No. 60/441,450, filed Jan.16, 2003, the specifications of which are incorporated herein in theirentirety.

STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSOREDRESEARCH AND DEVELOPMENT

This invention was made with government support under Grants GM44154,GM62159 and GM66494, all awarded by the National Institutes of Health,and under Grant DE-FG03-00ER45812, awarded by the Department of Energy(DOE). The Government has certain rights in the invention.

FIELD OF THE INVENTION

The invention is in the field of glycopeptides, glycoproteins, andrelated mimetics, and methods for synthesis of glycopeptides,glycoproteins, and related mimetics.

BACKGROUND OF THE INVENTION

The posttranslational modification of proteins by glycosylation canaffect protein folding and stability, modify the intrinsic activity ofproteins, and modulate their interactions with other biomolecules. See,e.g., Varki, A. (1993) Glycobiology 3:97-130. Natural glycoproteins areoften present as a population of many different glycoforms, which makesanalysis of glycan structure and the study of glycosylation effects onprotein structure and function difficult. Therefore, methods for thesynthesis of natural and unnatural homogeneously glycosylated proteinsare needed for the systematic understanding of glycan function, and forthe development of improved glycoprotein therapeutics.

One previously known approach for making proteins having desiredglycosylation patterns makes use of glycosidases to convert aheterogeneous natural glycoprotein to a simple homogenous core, ontowhich saccharides can then be grafted sequentially withglycosyltransferases. See, e.g., Witte, K., et al., (1997) J. Am. Chem.Soc. 119:2114-2118. A limitation of this approach is that the primaryglycosylation sites are predetermined by the cell line in which theprotein is expressed. Alternatively, a glycopeptide containing thedesired glycan structure can be synthesized by solid phase peptidesynthesis. This glycopeptide can be coupled to other peptides orrecombinant protein fragments to afford a larger glycoprotein by nativechemical ligation, (see, e.g., Shin, Y., et al., (1999) J. Am. Chem.Soc. 121:11684-11689) expressed protein ligation, (see, e.g., Tolbert,T. J. and Wong, C.-H. (2000) J. Am. Chem. Soc. 122:5421-5428), or withengineered proteases. See, e.g., Witte, K., et al., (1998) J. Am. Chem.Soc. 120:1979-1989. Both native chemical ligation and expressed proteinligation are most effective with small proteins, and necessitate acysteine residue at the N-terminus of the glycopeptide. When a proteaseis used to ligate peptides together, the ligation site must be placedfar away from the glycosylation site for good coupling yields. See,e.g., Witte, K., et al., (1998) J. Am. Chem. Soc. 120:1979-1989. A thirdapproach is to modify proteins with saccharides directly using chemicalmethods. Good selectivity can be achieved with haloacetamide saccharidederivatives, which are coupled to the thiol group of cysteine, (see,e.g., Davis, N. J. and, Flitsch, S. L. (1991) Tetrahedron Lett.32:6793-6796; and, Macmillan, D.; et al., (2002) Org Lett 4:1467-1470),but this method can become problematic with proteins that have more thanone cysteine residue.

Accordingly, a need exists for improved methods for making glycoproteinshaving a desired glycosylation pattern. The invention fulfills this andother needs, as will be apparent upon review of the followingdisclosure.

SUMMARY OF THE INVENTION

The invention provides methods for synthesis of glycoproteins. Thesemethods involve, in some embodiments, incorporating into a protein anunnatural amino acid that comprises a first reactive group; andcontacting the protein with a saccharide moiety that comprises a secondreactive group, wherein the first reactive group reacts with the secondreactive group to attach the saccharide moiety to the unnatural aminoacid. Glycoproteins produced by these methods are also included in theinvention. The first reactive group is, in some embodiments, anelectrophilic moiety (e.g., a keto moiety, an aldehyde moiety, and/orthe like) and the second reactive group is a nucleophilic moiety. Insome embodiments, the first reactive group is a nucleophilic moiety andthe second reactive group is an electrophilic moiety (e.g., a ketomoiety, an aldehyde moiety, and/or the like). For example, anelectrophilic moiety is attached to the saccharide moiety and thenucleophilic moiety is attached to the unnatural amino acid. Thesaccharide moiety can include a single carbohydrate moiety, or thesaccharide moiety can include two or more carbohydrate moieties.

In some embodiments, the methods further involve contacting thesaccharide moiety with a glycosyltransferase, a sugar donor moiety, andother reactants required for glycosyltransferase activity for asufficient time and under appropriate conditions to transfer a sugarfrom the sugar donor moiety to the saccharide moiety. The product ofthis reaction can, if desired, be contacted by at least a secondglycosyltransferase, together with the appropriate sugar donor moiety.

In certain embodiments, the method further comprises contacting thesaccharide moiety with one or more of aβ1-4N-acetylglucosaminyltransferase, an α1,3fucosyltransferase, an α1,2fucosyltransferase, an α1,4fucosyltransferase, aβ1-4galactosyltransferase, a sialyltransferase, and/or the like, to forma biantennary or triantennary oligosaccharide structure.

In one embodiment, the saccharide moiety comprises a terminal GlcNAc,the sugar donor moiety is UDP-Gal and the glycosyltransferase is aβ-1,4-galactosyltransferase. In one embodiment, the saccharide moietycomprises a terminal GlcNAc, the sugar donor moiety is UDP-GlcNAc andthe glycosyltransferase is a β1-4N-acetylglucosaminyltransferase.Optionally, the method further comprises contacting the product of theN-acetylglucosaminyltransferase reaction with a β1-4mannosyltransferaseand GDP-mannose to form a saccharide moiety that comprisesManβ1-4GlcNAcβ1-4GlcNAc-. Optionally, the method further comprisescontacting the Manβ1-4GlcNAcβ1-4GlcNAc-moiety with anα1-3mannosyltransferase and GDP-mannose to form a saccharide moiety thatcomprises Manα1-3Manβ1-4GlcNAcβ1-4GlcNAc-. Optionally, the methodfurther comprises contacting the Manα1-3Manβ1-4GlcNAcβ1-4GlcNAc-moietywith an α1-6mannosyltransferase and GDP-mannose to form a saccharidemoiety that comprises Manα1-6(Manα1-3)Manα1-4GlcNAcβ1-4GlcNAc-.Optionally, the method further comprises contacting theManα1-6(Manα1-3)Manβ1-4GlcNAcβ1-4GlcNAc-moiety with aβ1-2N-acetylglucosaminyltransferase and UDP-GlcNAc to form a saccharidemoiety that comprisesManα1-6(GlcNAcβ1-2Manα1-3)Manβ1-4GlcNAcβ1-4GlcNAc-. Optionally, themethod further comprises contacting theManα1-6(GlcNAcβ1-2Manα1-3)Manβ1-4GlcNAcβ1-4GlcNAc-moiety with aβ1-2N-acetylglucosaminyltransferase and UDP-GlcNAc to form a saccharidemoiety that comprisesGlcNAcβ1-2Manα1-6(GlcNAcβ1-2Manα1-3)Manβ1-4GlcNAcβ1-4GlcNAc-.

The step of incorporating into a protein an unnatural amino acid thatcomprises a first reactive group, in some embodiments, comprises usingan orthogonal tRNA/orthogonal aminoacyl-tRNA synthetase (O-tRNA/O-RS)pair, where the O-tRNA recognizes a selector codon and incorporates theunnatural amino acid into the protein in response to the selector codon,and wherein the O-RS preferentially aminoacylates the O-tRNA with theunnatural amino acid. For example, the O-RS comprises an amino acidsequence comprising any one of SEQ ID NO.: 1, 2 or 3. Optionally, theO-tRNA comprises a mutRNA_(CUA) ^(Tyr). In some embodiments, theunnatural amino acid is incorporated into the polypeptide in vivo.

The invention also provides glycoproteins that comprise a saccharidemoiety and a polypeptide. In certain embodiments in the glycoproteins ofthe invention, the saccharide moiety is attached to the polypeptide by areaction product of a nucleophilic reaction between a first reactivegroup attached to an unnatural amino acid present in the polypeptide anda second reactive group attached to the saccharide moiety. In certainembodiments, the first reactive group is an electrophilic moiety (e.g.,keto moiety, aldehyde moiety, and/or the like) and the second reactivegroup is a nucleophilic moiety.

In certain embodiments, the nucleophilic moiety of the inventionincludes, but is not limited to, hydrazide, hydroxylamine,semicarbazide, carbohydrazide, sulfonylhydrazide, and the like. Forexample, nucleophilic moieties include, but are not limited to, e.g.,—NR¹—NH₂(hydrazide), —NR¹(C═O)NR²NH₂ (semicarbazide), —NR¹(C═S)NR²NH₂(thiosemicarbazide), —(C═O)NR¹NH₂ (carbonylhydrazide), —C═S)NR¹NH₂(thiocarbonylhydrazide), —(SO₂)NR¹NH₂ (sulfonylhydrazide),—NR¹NR²(C═O)NR³NH₂ (carbazide), NR¹NR²(C═)NR³NH₂ (thiocarbazide), —O—NH₂(hydroxylamine), and the like, where each R¹, R², and R³ isindependently H, or alkyl having 1-6 carbons.

In certain embodiments of the invention, a reaction product of theinvention comprises, e.g., an oxime, an amide, a hydrazone, a reducedhydrazone, a carbohydrazone, a thiocarbohydrazone, a sufonylhydrazone, asemicarbazone, a thiosemicarbazone, and the like.

Other aspects of the invention include methods for synthesis of aglycoprotein by incorporating into a protein an unnatural amino acidthat comprises a saccharide moiety. A glycoprotein produced by themethod is also a feature of the invention. In certain embodiments, theincorporating step comprises using an orthogonal tRNA/orthogonalaminoacyl-tRNA synthetase (O-tRNA/O-RS) pair, wherein the O-tRNArecognizes a selector codon and incorporates the unnatural amino acidthat comprises a saccharide moiety (e.g., a β-O-GlcNAc-L-serine, atri-acetyl-β-GlcNAc-serine, a tri-O-acetyl-GalNAc-α-threonine, anα-GalNAc-L-threonine, and/or the like) into the protein in response tothe selector codon, and wherein the O-RS preferentially aminoacylatesthe O-tRNA with the unnatural amino acid. In one embodiment, theincorporating step is performed in vivo. For example, the O-RS comprisesan amino acid sequence comprising any one of SEQ ID NO.: 4, 5 or 6, oris encoded by a polynucleotide comprising a polynucleotide sequence ofany one of SEQ ID NO.: 8, 9, or 10. Optionally, the O-tRNA comprises amutRNA_(CUA) ^(Tyr). These methods can further involve contacting thesaccharide moiety with a glycosyltransferase, a sugar donor moiety, andother reactants required for glycosyltransferase activity for asufficient time and under a a sugar from the sugar donor moiety to thesaccharide moiety.

In certain embodiments, the method further comprises contacting theproduct of the glycosyltransferase reaction with at least a secondglycosyltransferase and a second sugar donor moiety. In one embodiment,the saccharide moiety comprises a terminal GlcNAc, the sugar donormoiety is UDP-GlcNAc and the glycosyltransferase is aβ1-4N-acetylglucosaminyltransferase. In another embodiment, thesaccharide moiety comprises a terminal GlcNAc, the sugar donor moiety isUDP-Gal and the glycosyltransferase is a 1 galactosyltransferase.Additional sugars can be added.

In certain embodiments, a glycosyltransferase of the invention includes,but is not limited to, e.g., a galactosyltransferase, afucosyltransferase, a glucosyltransferase, anN-acetylgalactosaminyltransferase, an N-acetylglucosaminyltransferase, aglucuronyltransferase, a sialyltransferase, a mannosyltransferase, aglucuronic acid transferase, a galacturonic acid transferase, anoligosaccharyltransferase, and the like.

The invention also provides host cells (e.g., mammalian cells, yeastcells, bacterial cells, plant cells, fungal cells, archaebacterialcells, insect cells, and/or the like) that are useful for synthesizing aglycoprotein. These host cells contain: a) an unnatural amino acid thatcomprises a saccharide moiety; b) an orthogonal tRNA that recognizes aselector codon; c) an orthogonal aminoacyl tRNA synthetase (O-RS) thatcatalyzes attachment of the unnatural amino acid to the orthogonal tRNA;d) a polynucleotide that encodes a glycosyltransferase; and e) apolynucleotide sequence that encodes a polypeptide and comprises atleast one selector codon.

Also provided by the invention are compositions that include atranslation system. The translation systems include an orthogonal tRNA(O-tRNA) and an orthogonal aminoacyl tRNA synthetase (O-RS), wherein theO-RS preferentially aminoacylates the O-tRNA with an unnatural aminoacid that comprises a saccharide moiety (e.g., a β-O-GlcNAc-L-serine, atri-acetyl-β-GlcNAc-serine, a tri-O-acetyl-GalNAc-α-threonine, anα-GalNAc-L-threonine, and/or the like) and the O-tRNA recognizes atleast one selector codon. In certain embodiments, the O-RS comprises anamino acid sequence comprising any one of SEQ ID NO.: 4, 5 or 6, or isencoded by a polynucleotide comprising a polynucleotide sequence of anyone of SEQ ID NO.: 8, 9, or 10. Optionally, the O-tRNA comprises amutRNA_(CUA)^(Tyr).

Artificial (e.g., man-made, and not naturally occurring) polypeptidesand polynucleotides are also features of the invention. For example, anartificial polypeptide of the invention includes, e.g., (a) apolypeptide that comprises an amino acid sequence as shown in any one ofSEQ ID NO.: 4-6; (b) a polypeptide that comprises an amino acid sequenceencoded by a polynucleotide sequence as shown in any one of SEQ ID NO.:8-10; (c) a polypeptide that is specifically immunoreactive with anantibody specific for a polypeptide of (a), or (b); and, (d) an aminoacid sequence comprising a conservative variation of (a), (b), or (c).Antibodies and antisera that are specifically immunoreactive with anartificial polypeptide of the invention are also provided. An artificialpolynucleotide of the invention includes, e.g., (a) a polynucleotidecomprising a nucleotide sequence as set forth in any one of SEQ ID NO.:8-10; (b) a polynucleotide that is complementary to or that encodes apolynucleotide sequence of (a); (c) a polynucleotide encoding apolypeptide that comprises an amino acid sequence as set forth in anyone of SEQ ID NO.: 1-6, or a conservative variation thereof; (d) apolynucleotide that encodes an artificial polypeptide; (e) a nucleicacid that hybridizes to a polynucleotide of (a), (b), (c), or (d) underhighly stringent conditions over substantially the entire length of thenucleic acid; (f) a polynucleotide that is at least 98% identical to apolynucleotide of (a), (b), (c), (d), or (e); and, (h) a polynucleotidecomprising a conservative variation of (a), (b), (c), (d), (e), or (f).

DEFINITIONS

Before describing the invention in detail, it is to be understood thatthis invention is not limited to particular devices or biologicalsystems, which can, of course, vary. It is also to be understood thatthe terminology used herein is for the purpose of describing particularembodiments only, and is not intended to be limiting. As used in thisspecification and the appended claims, the singular forms “a”, “an” and“the” include plural referents unless the content clearly dictatesotherwise. Thus, for example, reference to “a cell” includes acombination of two or more cells; reference to “bacteria” includesmixtures of bacteria, and the like.

Orthogonal: As used herein, the term “orthogonal” refers to a molecule(e.g., an orthogonal tRNA (O-tRNA) and/or an orthogonal aminoacyl tRNAsynthetase (O-RS)) that is used with reduced efficiency by acorresponding molecule that is endogenous to a cell or other translationsystem. Orthogonal refers to the inability or reduced efficiency, e.g.,less than 20% efficiency, less than 10% efficiency, less than 5%efficiency, or less than 1% efficiency, of an orthogonal tRNA tofunction with an endogenous tRNA synthetase, or of an orthogonal RS tofunction with an endogenous tRNA in the translation system of interest.For example, an orthogonal tRNA in a translation system of interest isaminoacylated by any endogenous RS of a translation system of interestwith reduced or even zero efficiency, when compared to aminoacylation ofan endogenous tRNA by the endogenous RS. In another example, anorthogonal RS aminoacylates any endogenous tRNA in the translationsystem of interest with reduced or even zero efficiency, as compared toaminoacylation of the endogenous tRNA by an endogenous RS.

Preferentially aminoacylates: The term “preferentially aminoacylates”refers to an efficiency of, e.g., about 70% efficiency, about 75%efficiency, about 85% efficiency, about 90% efficiency, about 95%efficiency, or e.g., about 99% or more efficiency, at which an O-RSaminoacylates an O-tRNA with an unnatural amino acid compared to anaturally occurring tRNA or starting material used to generate theO-tRNA. The unnatural amino acid is then incorporated into a growingpolypeptide chain with high fidelity, e.g., at greater than about 75%efficiency for a given selector codon, at greater than about 80%efficiency for a given selector codon, at greater than about 90%efficiency for a given selector codon, at greater than about 95%efficiency for a given selector codon, or at greater than about 99% ormore efficiency for a given selector codon.

Selector codon: The term “selector codon” refers to codons recognized byan O-tRNA in the translation process and not typically recognized by anendogenous tRNA. The O-tRNA anticodon loop recognizes the selector codonon the mRNA and incorporates its amino acid, e.g., an unnatural aminoacid, at this site in the polypeptide. Selector codons can include,e.g., nonsense codons, such as stop codons, e.g., amber, ochre, and opalcodons; four or more base codons; codons derived from natural orunnatural base pairs and/or the like. For a given system, a selectorcodon can also include one of the natural three base codons, wherein theendogenous system does not use said natural three base codon, e.g., asystem that is lacking a tRNA that recognizes the natural three basecodon or a system wherein the natural three base codon is a rare codon.

Suppressor tRNA: A suppressor tRNA is a tRNA that alters the reading ofa messenger RNA (mRNA) in a given translation system. A suppressor tRNAcan read through, e.g., a stop codon, a four base codon, a rare codon,and/or the like.

Translation system: The term “translation system” refers to thecomponents necessary to incorporate a naturally occurring amino acidinto a growing polypeptide chain (protein). Components of a translationsystem can include, e.g., ribosomes, tRNAs, synthetases, mRNA and thelike. The components of the invention can be added to a translationsystem, in vivo or in vitro. A translation system can be a cell, eitherprokaryotic, e.g., an E. coli cell, Archael cell, etc. or eukaryotic,e.g., a yeast, mammalian, plant, insect cell, etc.

Unnatural amino acid: As used herein, the term “unnatural amino acid”refers to any amino acid, modified amino acid, and/or amino acidanalogue that is not one of the 20 naturally occurring amino acids orseleno cysteine or pyrrolysine.

Saccharide moiety: As used herein, the term “saccharide moiety” refersto natural and unnatural sugar moieties (i.e., a non-naturally occuringsugar moiety, e.g., a sugar moiety that is modified, e.g., at one ormore hydroxyl or amino positions, e.g., dehydroxylated, deaminated,esterified, etc., e.g., 2-deoxyGal is an example of an unnatural sugarmoiety). The term “carbohydrate” has the general formula (CH₂O)_(n), andincludes, but is not limited to, e.g., monosaccharides, disaccharides,oligosaccharides and polysaccharides. Oligosaccharides are chainscomposed of saccharide units, which are alternatively known as sugars.Saccharide units can be arranged in any order and the linkage betweentwo saccharide units can occur in any of approximately ten differentways.

The following abbreviations are used herein:

-   -   Ara=arabinosyl;    -   Fru=fructosyl;    -   Fuc=fucosyl;    -   Gal=galactosyl;    -   GalNAc=N-acetylgalactosaminyl;    -   Glc=glucosyl;    -   GlcNAc=N-acetylglucosaminyl;    -   Man=mannosyl; and    -   NeuAc=sialyl (typically N-acetylneuraminyl).

Oligosaccharides are considered to have a reducing end and anon-reducing end, whether or not the saccharide at the reducing end isin fact a reducing sugar. In accordance with accepted nomenclature,oligosaccharides are depicted herein with the non-reducing end on theleft and the reducing end on the right. All oligosaccharides describedherein are described with the name or abbreviation for the non-reducingsaccharide (e.g., Gal), followed by the configuration of the glycosidicbond (α or β), the ring bond, the ring position of the reducingsaccharide involved in the bond, and then the name or abbreviation ofthe reducing saccharide (e.g., GlcNAc). The linkage between two sugarsmay be expressed, for example, as 2,3, 2→3,2-3, or (2,3). Natural andunnatural linkages (e.g., 1-2, 1-3, 1-4, 1-6, 2-3, 2-4, 2-6, etc.)between two sugars are included in the invention. Each saccharide is apyranose.

The term “sialic acid” (abbreviated “Sia”) refers to any member of afamily of nine-carbon carboxylated sugars. The most common member of thesialic acid family is N-acetyl-neuraminic acid(2-keto-5-acetamindo-3,5-dideoxy-D-glycero-D-galactononulopyranos-1-onicacid) (often abbreviated as Neu5Ac, NeuAc, or NANA). A second member ofthe family is N-glycolyl-neuraminic acid (Neu5Gc or NeuGc), in which theN-acetyl group of NeuAc is hydroxylated. A third sialic acid familymember is 2-keto-3-deoxy-nonulosonic acid (KDN) (Nadano et al. (1986) J.Biol. Chem. 261: 11550-11557; Kanamori et al. (1990) J. Biol. Chem. 265:21811-21819. Also included are 9-substituted sialic acids such as a9-O—C₁-C₆ acyl-Neu5Ac like 9-O-lactyl-Neu5Ac or 9-O-acetyl-Neu5Ac,9-deoxy-9-fluoro-Neu5Ac and 9-azido-9-deoxy-Neu5Ac. For review of thesialic acid family, see, e.g., Varki (1992) Glycobiology 2: 25-40;Sialic Acids: Chemistry. Metabolism and Function, R. Schauer, Ed.(Springer-Verlag, New York (1992). The synthesis and use of sialic acidcompounds in a sialylation procedure is described in, for example,international application WO 92/16640, published Oct. 1, 1992.

Donor substrates for glycosyltransferases are activated nucleotidesugars. Such activated sugars generally consist of uridine and guanosinediphosphate, and cytidine monophosphate, derivatives of the sugars inwhich the nucleoside diphosphate or monophosphate serves as a leavinggroup. Bacterial, plant, and fungal systems can sometimes use otheractivated nucleotide sugars.

Unless otherwise defined herein or below in the remainder of thespecification, all technical and scientific terms used herein have thesame meaning as commonly understood by those of ordinary skill in theart to which the invention belongs.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 schematically illustrates examples of two schemes (a sequentialroute and a convergent route) for attaching a saccharide moiety to apolypeptide that includes an unnatural amino acid.

FIG. 2 illustrates HPLC analysis of the coupling reaction betweenaminooxy saccharide 1 (of FIG. 1) and mutant Z domain protein I (ofFIG. 1) containing p-acetyl-L-phenylalanine at 7 hours and 26 hours.

FIG. 3 illustrates high-resolution MALDI-FTICR MS spectra of mutant Zdomain protein I (of FIG. 1), glycoprotein mimetics II, III, and IV (ofFIG. 1). The 2⁺ isotopic cluster of each spectrum is shown.

FIG. 4 illustrates expression of the Gly4→A mutant myoglobin (˜18.5 kD).Proteins were purified by Ni²⁺-affinity chromatography and resolved bySDS-PAGE. The gel was silver-stained.

FIG. 5 illustrates MALDI-TOF analysis of the molecular weight of theGly4→A mutant myoglobin.

FIG. 6, Panel A, B and C illustrate characterization of the purifiedmutant myoglobin containing a glycosylated amino acid. Panel Aillustrates binding of a GlcNAc-specific lectin, Banderiraeasimplicifolia II (BSII), to wild-type myoglobin and glycomyoglobin.Panel B illustrates on-blot galactosyltransferase labelingglycomyoglobin with UDP-[H³]galactose. Panel C illustrates quantitativeanalysis of the galactosyltransferase reaction, which was carried out insolution, and the radiolabeled galactose was normalized such that 1.0corresponds to 100% transfer.

DETAILED DESCRIPTION

Posttranslational modifications of proteins regulate many biologicalprocesses, including metabolism, signal transduction, and geneexpression. The synthetic challenges associated with generatinghomogeneous populations of selectively modified proteins, however, havehindered detailed studies of the effects of these modifications onprotein structure and function. For example, glycosylation is one of themost common post-translational modifications of proteins in eukaryotesand affects a wide range of protein functions from folding and secretionto biomolecular recognization and serum half life. See, e.g., R. A.Dwek, (1996) Chem. Rev. 96:683. While there have been significantadvances in our understanding of the effects of glycosylation, thespecific roles of oligosaccharide chains and the relationships betweentheir structures and functions are just beginning to be understood. See,e.g, C. R. Bertozzi, & L. L. Kiessling, (2001) Science 291:2357. Theprimary challenge is that glycoproteins are typically produced as amixture of glycoforms, making it difficult to isolate unique glycoformsfrom natural sources. A variety of methods have been developed tosynthesize structurally defined glycoforms, but all impose severerestrictions on the size, quantity, and/or quality of the glycoproteinproduced. See, e.g., P. Sears, & C. H. Wong, (2001) Science 291:2344; M.Wacker et al., (2002) Science 298:1790; B. G. Davis, (2002) Chem. Rev.102:579; and, H. C. Hang, & C. R. Bertozzi, (2001) Acc. Chem. Res.34:727. The invention solves this and other problems, and providesglycoproteins and glycoprotein mimetics, and methods for synthesis ofglycoproteins having desired glycosylation patterns. The glycoproteinsand glycoprotein mimetics of the invention have utility in producinghomogeneous glycoforms of therapeutic glycoproteins and/or facilitatingthe studies on the structures and functions of glycosylated proteins.

Glycosylation

The invention provides methods for synthesizing glycoproteins. Incertain embodiments, these methods involve incorporating into theprotein an unnatural amino acid that comprises a first reactive group;and reacting the first reactive group with a second reactive group thatis attached to a saccharide moiety, thereby forming a covalent bond andattaching the saccharide moiety to the protein.

A wide variety of suitable reactive groups are known to those of skillin the art. Such suitable reactive groups can include, for example,amino, hydroxyl, carboxyl, carboxylate, carbonyl, alkenyl, alkynyl,aldehyde, ester, ether (e.g. thio-ether), amide, amine, nitrile, vinyl,sulfide, sulfonyl, phosphoryl, or similarly chemically reactive groups.Additional suitable reactive groups include, but are not limited to,maleimide, N hydroxysuccinimide, sulfo-N-hydroxysuccinimide,nitrilotriacetic acid, activated hydroxyl, haloacetyl (e.g.,bromoacetyl, iodoacetyl), activated carboxyl, hydrazide, epoxy,aziridine, sulfonylchloride, trifluoromethyldiaziridine,pyridyldisulfide, N-acyl-imidazole, imidazolecarbamate, vinylsulfone,succinimidylcarbonate, arylazide, anhydride, diazoacetate, benzophenone,isothiocyanate, isocyanate, imidoester, fluorobenzene, biotin andavidin.

In some embodiments, one of the reactive groups is an electrophilicmoiety, and the second reactive group is a nucleophilic moiety. Eitherthe nucleophilic moiety or the electrophilic moiety can be attached tothe side chain of the unnatural amino acid; the corresponding group isthen attached to the saccharide moiety. Suitable electrophilic moietiesthat react with nucleophilic moieties to form a covalent bond are knownto those of skill in the art. Such electrophilic moieties include, butare not limited to, e.g., carbonyl group, a sulfonyl group, an aldehydegroup, a ketone group, a hindered ester group, a thioester group, astable imine group, an epoxide group, an aziridine group, etc. Suitablenucleophilic moieties that can react with electrophilic moiety are knownto those of skill in the art. Such nucleophiles include, for example,aliphatic or aromatic amines, such as ethylenediamine. In otherembodiments, the reactive group is —NR¹—NH₂ (hydrazide), —NR¹(C═O)NR²NH₂(semicarbazide), —NR¹(CS)NR²NH₂ (thiosemicarbazide), —(C═O)NR¹NH₂(carbonylhydrazide), —(C═S)NR¹NH₂ (thiocarbonylhydrazide), —(SO₂)NR¹NH₂(sulfonylhydrazide), —NR¹NR²(C═O)NR³NH₂ (carbazide), —NR¹NR²(C═S)NR³NH₂(thiocarbazide), —O—NH₂ (hydroxylamine), and/or the like, where each R¹,R², and R³ is independently H, or an alkyl moiety having 1-6 carbons,preferably H. In one aspect of the invention, the reactive group is ahydrazide, hydroxylamine, semicarbazide, carbohydrazide, asulfonylhydrazide, or the like.

The product of the reaction between the nucleophile and theelectrophilic moiety typically incorporates the atoms originally presentin the nucleophilic moiety. Typical linkages obtained by reacting thealdehydes or ketones with the nucleophilic moieties include reactionproducts such as an oxime, an amide, a hydrazone, a reduced hydrazone, acarbohydrazone, a thiocarbohydrazone, a sufonylhydrazone, asemicarbazone, a thiosemicarbazone, or similar functionality, dependingon the nucleophilic moiety used and the electrophilic moiety (e.g.,aldehyde, ketone, and/or the like) that is reacted with the nucleophilicmoiety. Linkages with carboxylic acids are typically referred to ascarbohydrazides or as hydroxamic acids. Linkages with sulfonic acids aretypically referred to as sulfonylhydrazides or N-sulfonylhydroxylamines.The resulting linkage can be subsequently stabilized by chemicalreduction.

In certain embodiments, the glycoprotein is synthesized by incorporatingan unnatural amino acid, to which is attached a saccharide moiety, intoa polypeptide. For example, an orthogonal O-tRNA/O-RS can be utilizedthat incorporates the unnatural amino acid with the saccharide moietyinto a growing polypeptide chain in response to a selector codon. See,e.g., section herein entitled. “Preparation of Proteins Having anUnnatural Amino Acid.”

Glycosyltransferases

The invention provides methods in which an amino acid-linked saccharidemoiety or an unnatural amino acid that includes a saccharide moiety isfurther glycosylated. These glycosylation steps are preferably carriedout enzymatically using, for example, a glycosyltransferase,glycosidase, or other enzyme known to those of skill in the art. In someembodiments, a plurality of enzymatic steps are carried out in a singlereaction mixture that contains two or more differentglycosyltransferases. For example, one can conduct a galactosylating anda sialylating step simultaneously by including both sialyltransferaseand galactosyltransferase in the reaction mixture.

For enzymatic saccharide syntheses that involve glycosyltransferasereactions, the recombinant cells of the invention optionally contain atleast one heterologous gene that encodes a glycosyltransferase. Manyglycosyltransferases are known, as are their polynucleotide sequences.See, e.g., “The WWW Guide To Cloned Glycosyltransferases,” (available onthe World Wide Web at www.vei.co.uk/TGN/gt_guide.htm).Glycosyltransferase amino acid sequences and nucleotide sequencesencoding glycosyltransferases from which the amino acid sequences can bededuced are also found in various publicly available databases,including GenBank, Swiss-Prot, EMBL, and others.

Glycosyltransferases that can be employed in the cells of the inventioninclude, but are not limited to, galactosyltransferases,fucosyltransferases, glucosyltransferases,N-acetylgalactosaminyltransferases, N-acetylglucosaminyltransferases,glucuronyltransferases, sialyltransferases, mannosyltransferases,glucuronic acid transferases, galacturonic acid transferases,oligosaccharyltransferases, and the like. Suitable glycosyltransferasesinclude those obtained from eukaryotes, as well as from prokaryotes.

An acceptor for the glycosyltransferases will be present on theglycoprotein to be modified by the methods of the invention. Suitableacceptors, include, for example, galactosyl acceptors such asGalβ1,4GalNAc-, Galβ1,3GalNAc-, lacto-N-tetraose-, Galβ1,3GlcNAc-,Galβ1,4GlcNAc-, Galβ1,3Ara-, Galβ1,6GlcNAc-, and Galβ1,4Glc-(lactose).Other acceptors known to those of skill in the art (see, e.g., Paulsonet al. (1978) J. Biol. Chem. 253: 5617-5624). Typically, the acceptorsform part of a saccharide moiety chain that is attached to theglycoprotein.

Enzyme amounts or concentrations are expressed in activity Units, whichis a measure of the initial rate of catalysis. One activity Unitcatalyzes the formation of 1 μmol of product per minute at a giventemperature (typically 37° C.) and pH value (typically 7.5). Thus, 10Units of an enzyme is a catalytic amount of that enzyme where 10 μmolsof substrate are converted to 10 μmol of product in one minute at atemperature of 37° C. and a pH value of 7.5. The enzymes can be utilizedfree in solution or can be bound to a support such as a polymer. Thereaction mixture is thus substantially homogeneous at the beginning,although some precipitate can form during the reaction.

The glycosylation reactions include, in addition to the appropriateglycosyltransferase and acceptor, an activated nucleotide sugar thatacts as a sugar donor for the glycosyltransferase. The reactions canalso include other ingredients that facilitate glycosyltransferaseactivity. These ingredients can include a divalent cation (e.g., Mg⁺² orMn⁺²), materials necessary for ATP regeneration, phosphate ions, andorganic solvents. The concentrations or amounts of the various reactantsused in the processes depend upon numerous factors including reactionconditions such as temperature and pH value, and the choice and amountof acceptor saccharides to be glycosylated. The reaction medium may alsocomprise solubilizing detergents (e.g., Triton or SDS) and organicsolvents such as methanol or ethanol, if necessary.

Oligosaccharides produced using the methods of the invention can beanalyzed by methods that are known to those of skill in the art. Forexample, the carbohydrate units can be released from the carbohydratemoieties by alkaline β-elimination, for example, and separated from thepolypeptide by gel filtration. The resulting oligosaccharides are thenseparated from each other using a one or more standard techniques, suchas of gel filtration, HPLC, thin layer chromatography, and ion exchangechromatography, or a combination thereof, and can be fully analyzed.Complete structural analysis of the purified oligosaccharide unitsrequires the determination of the monosaccharide units, their ring form,configuration (D or L), anomeric linkage (α or β), the positions of thelinkages between the sugars and their sequence. In addition, theposition of any substituent groups are established. Methylation analysiscan be used to determine the positions of the glycosidic linkagesbetween the monosaccharides. The anomeric configuration of the sugarresidues can be addressed using, e.g., ¹H NMR spectroscopy. Theconditions and methods used to perform a complete structuralcarbohydrate analysis are described generally in Beeley, LaboratoryTechniques in Biochemistry and Molecular Biology, eds. Burdon andKnippenberg, Elsevier, Amsterdam (1985), Hounsell, “GlycoanalysisProtocols”, Meth. Mol. Biol. Vol. 76, 1998, and El Rassi, CarbohydrateAnalysis: High Performance Liquid Chromatography and CapillaryElectrophoresis, Elsevier Science Ltd, Vol. 58 (1994).

Additional techniques to fully characterize the sugars of anoligosaccharide include FAB-MS (fast atom bombardment-massspectrometry), HPAE (high pH anion exchange chromatography) and NMR(nuclear magnetic resonance spectroscopy, particularly ¹H-NMR and¹³C-NMR). These techniques are complementary. Examples of how thesetechniques are used to fully characterize the structure of anoligosaccharide can be found in the analysis by Spellman et al., (1989)J. Biol. Chem. 264: 14100, and Stanley et al. (1988) J. Biol. Chem. 263:11374. Other methods include positive ion fast atom bombardment massspectroscopy (FAB-MS) and methylation analysis by gaschromatography-electron impact mass spectroscopy (GC/EI-MS) (see EPOApplication No. 89305153.2).

In Vivo Synthesis of Glycoproteins

To synthesize a glycoprotein in vivo, one can introduce into anexpression vector a polynucleotide that encodes a polypeptide ofinterest. The polynucleotide also includes one or more selector codonsat the positions at which attachment of a saccharide moiety is desired.The expression vector is introduced into a host cell that includes anunnatural amino acid, e.g., an unnatural amino acid comprising a moietywhere a saccharide moiety can be attached, such as an aldehyde- orketo-derivatized amino acid, or an unnatural amino acid that includes asaccharide moiety; an orthogonal tRNA that recognizes the selectorcodon; and an orthogonal aminoacyl tRNA synthetase (O-RS) that catalyzesattachment of the unnatural amino acid to the orthogonal tRNA. The O-RSattaches the unnatural amino acid to the orthogonal tRNA, which thenintroduces the unnatural amino acid into the nascent protein.

In some embodiments, the host cell further includes one or morepolynucleotides that encode glycosyltransferases. Such host cells cancatalyze the addition of one or more sugars to the saccharide moietythat is attached to the unnatural amino acid.

Several well-known methods of introducing target nucleic acids intobacterial cells are available, any of which can be used in theinvention. These include: fusion of the recipient cells with bacterialprotoplasts containing the DNA, electroporation, projectile bombardment,and infection with viral vectors, etc. Bacterial cells can be used toamplify the number of plasmids containing DNA constructs of thisinvention. The bacteria are grown to log phase and the plasmids withinthe bacteria can be isolated by a variety of methods known in the art(see, for instance, Sambrook, infra). In addition, a plethora of kitsare commercially available for the purification of plasmids frombacteria, (see, e.g., EasyPrep™, FlexiPrep™, both from PharmaciaBiotech; StrataClean™, from Stratagene; and, QIAprep™ from Qiagen). Theisolated and purified plasmids are then further manipulated to produceother plasmids, used to transfect cells or incorporated into relatedvectors to infect organisms.

The engineered host cells can be cultured in conventional nutrient mediamodified as appropriate for such activities as, for example, screeningsteps, activating promoters or selecting transformants. These cells canoptionally be cultured into transgenic organisms.

Other useful references, e.g. for cell isolation and culture (e.g., forsubsequent nucleic acid isolation) include Freshney (1994) Culture ofAnimal Cells, a Manual of Basic Technique, third edition, Wiley-Liss,New York and the references cited therein; Payne et al. (1992) PlantCell and Tissue Culture in Liquid Systems, John Wiley & Sons, Inc. NewYork, N.Y.; Gamborg and Phillips (eds) (1995) Plant Cell, Tissue andOrgan Culture; Fundamental Methods Springer Lab Manual, Springer-Verlag(Berlin Heidelberg New York) and Atlas and Parks (eds) The Handbook ofMicrobiological Media (1993) CRC Press, Boca Raton, Fla.

General texts which describe molecular biological techniques includeBerger and Kimmel, Guide to Molecular Cloning Techniques. Methods inEnzymology volume 152 Academic Press, Inc., San Diego, Calif. (Berger);Sambrook et al., Molecular Cloning—A Laboratory Manual (3rd Ed.), Vol.1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 2001(“Sambrook”) and Current Protocols in Molecular Biology F. M. Ausubel etal., eds., Current Protocols, a joint venture between Greene PublishingAssociates, Inc. and John Wiley & Sons, Inc., (supplemented through2003) (“Ausubel”)). These texts describe mutagenesis, the use ofvectors, promoters and many other relevant topics related to, e.g., thegeneration of genes that include selector codons for production ofproteins that include unnatural amino acids, orthogonal tRNAs,orthogonal synthetases, and pairs thereof.

Preparation of Proteins having an Unnatural Amino Acid

Features of the invention include producing glycoproteins that includean unnatural amino acid, e.g., an unnatural amino acid comprising amoiety where a saccharide moiety can be attached, or an unnatural aminoacid that includes a saccharide moiety. In certain embodiments, theinvention involves producing glycoproteins that include one or moreunnatural amino acids to which are attached suitable reactive groupsthat can form a covalent bond when reacted with a second reactive group.In some embodiments, the unnatural amino acids comprise an electrophilicmoiety, e.g., aldehyde- or keto-derivatized amino acids, and thealdehyde- or keto-moieties are reacted with a nucleophilic moiety toattach a saccharide moiety to the polypeptide or protein. The unnaturalamino acid-containing proteins are synthesized by cells in which theprotein biosynthetic machinery has been altered to accommodateadditional genetically encoded amino acids using orthogonaltRNA/aminoacyl tRNA synthetase (O-tRNA/O-RS) pairs. In particular, thecells include an orthogonal tRNA that recognizes a selector codon (e.g.,stop codons, four base codons, and the like), and an orthogonalaminoacyl tRNA synthetase that can attach an aldehyde- orketo-derivatized amino acid to the orthogonal tRNA.

In certain embodiments, the invention involves producing glycoproteinsthat include one or more unnatural amino acids that includes asaccharide moiety. The unnatural amino acid-containing proteins aresynthesized by cells in which the protein biosynthetic machinery hasbeen altered to accommodate additional genetically encoded amino acidsusing orthogonal tRNA/aminoacyl tRNA synthetase (O-tRNA/O-RS) pairs. Inparticular, the cells include an orthogonal tRNA that recognizes aselector codon (e.g., stop codons, four base codons, and the like), andan orthogonal aminoacyl tRNA synthetase that can attach the unnaturalamino acid with the saccharide moiety to the orthogonal tRNA.

This technology allows the site-specific incorporation of the unnaturalamino acids directly into proteins in vivo. Importantly, the unnaturalamino acid is added to the genetic repertoire, rather than substitutingfor one of the common 20 amino acids. The protein can have one ormultiple (the same or different) unnatural amino acids at a particularposition in the protein. Unlike earlier methods for derivatizingproteins, the use of O-tRNA/O-RS pairs allows one to make proteinshaving an unnatural amino acid at only one of the locations at which aparticular amino acid occurs in a protein, if desired, rather thanderivatizing that particular amino acid at each location at which itoccurs in a protein.

To make a glycoprotein, one can use host cells and organisms that areadapted for the in vivo incorporation of the unnatural amino acid viaorthogonal tRNA/RS pairs. Host cells are genetically engineered (e.g.,transformed, transduced or transfected) with one or more vectors thatexpress the orthogonal tRNA, the orthogonal tRNA synthetase, and avector that encodes the protein to be derivatized. Each of thesecomponents can be on the same vector, or each can be on a separatevector, two components can be on one vector and the third component on asecond vector. The vector can be, for example, in the form of a plasmid,a bacterium, a virus, a naked polynucleotide, or a conjugatedpolynucleotide.

The coding regions for the orthogonal tRNA, the orthogonal tRNAsynthetase, and the protein to be derivatized are operably linked togene expression control elements that are functional in the desired hostcell. Typical vectors contain transcription and translation terminators,transcription and translation initiation sequences, and promoters usefulfor regulation of the expression of the particular target nucleic acid.The vectors optionally comprise generic expression cassettes containingat least one independent terminator sequence, sequences permittingreplication of the cassette in eukaryotes, or prokaryotes, or both(e.g., shuttle vectors) and selection markers for both prokaryotic andeukaryotic systems. Vectors are suitable for replication and/orintegration in prokaryotes, eukaryotes, or preferably both. See Giliman& Smith, Gene 8:81 (1979); Roberts, et al., Nature, 328:731 (1987);Schneider, B., et al., Protein Expr. Purif. 6435:10 (1995); Berger andKimmel, supra; Sambrook, supra, and Ausubel, supra. A catalogue ofBacteria and Bacteriophages useful for cloning is provided, e.g., by theATCC, e.g., The ATCC Catalogue of Bacteria and Bacteriophage (1992)Gherna et al. (eds) published by the ATCC. Additional basic proceduresfor sequencing, cloning and other aspects of molecular biology andunderlying theoretical considerations are also found in Watson et al.(1992) Recombinant DNA Second Edition Scientific American Books, NY.Proteins and Polypeptides of Interest.

For example, methods for producing glycoproteins include growing, in anappropriate medium, the cell, where the cell comprises a nucleic -acidthat comprises at least one selector codon and encodes a protein,providing an unnatural amino acid, e.g., an unnatural amino acidcomprising a moiety where a saccharide moiety can be attached, or anunnatural amino acid that includes a saccharide moiety, andincorporating the unnatural amino acid into the specified position inthe protein during translation of the nucleic acid with the at least oneselector codon, thereby producing the protein. The cell furthercomprises: an orthogonal-tRNA (O-tRNA) that functions in the cell andrecognizes the selector codon; and, an orthogonal aminoacyl-tRNAsynthetase (O-RS) that preferentially aminoacylates the O-tRNA with theunnatural amino acid, e.g., an unnatural amino acid comprising a moietywhere a saccharide moiety can be attached, or an unnatural amino acidthat includes a saccharide moiety. The publication WO 2002/085923,entitled “IN VIVO INCORPORATION OF UNNATURAL AMINO ACIDS” describes thisprocess and is incorporated herein by reference. For example, when anO-tRNA/O-RS pair is introduced into a host the pair leads to the in vivoincorporation of unnatural amino acid, e.g., an unnatural amino acidcomprising a moiety where a saccharide moiety can be attached, or anunnatural amino acid that includes a saccharide moiety, which can beexogenously added to the growth medium, into a protein, in response to aselector codon. Optionally, the compositions of the invention can be inan in vitro translation system, or in an in vivo system(s). See alsocorresponding application entitled “Site Specific Incorporation of KetoAmino Acids into Proteins,” filed Oct. 15, 2003, attorney docket number54-000170PCT, which is incorporated by reference.

A cell of the invention provides the ability to synthesize or produceglycoproteins in large useful quantities. In one aspect, the compositionoptionally includes, e.g., at least 10 micrograms, at least 50micrograms, at least 75 micrograms, at least 100 micrograms, at least200 micrograms, at least 250 micrograms, at least 500 micrograms, atleast 1 milligram, at least 10 milligrams or more of the glycoprotein,or an amount that can be achieved with in vivo protein productionmethods (details on recombinant protein production and purification areprovided herein). In another aspect, the protein is optionally presentin the composition at a concentration of, e.g., at least 10 microgramsof protein per liter, at least 50 micrograms of protein per liter, atleast 75 micrograms of protein per liter, at least 100 micrograms ofprotein per liter, at least 200 micrograms of protein per liter, atleast 250 micrograms of protein per liter, at least 500 micrograms ofprotein per liter, at least 1 milligram of protein per liter, or atleast 10 milligrams of protein per liter or more, in, e.g., a celllysate, a buffer, a pharmaceutical buffer, or other liquid suspension(e.g., in a volume of, e.g., anywhere from about 1 nl to about 100 L).The production of large quantities (e.g., greater that that typicallypossible with other methods, e.g., in vitro translation) of a protein ina cell including at least one unnatural amino acid, e.g., an unnaturalamino acid comprising a moiety where a saccharide moiety can beattached, or an unnatural amino acid that includes a saccharide moietyis a feature of the invention.

The incorporation of an unnatural amino acid, e.g., an unnatural aminoacid comprising a moiety where a saccharide moiety can be attached, oran unnatural amino acid that includes a saccharide moiety, can be doneto, e.g., tailor changes in protein structure and/or function, e.g., tochange size, acidity, nucleophilicity, hydrogen bonding, hydrophobicity,accessibility of protease target sites, target access to a proteinmoiety, etc. Proteins that include an unnatural amino acid, e.g., anunnatural amino acid comprising a moiety where a saccharide moiety canbe attached, or an unnatural amino acid that includes a saccharidemoiety, can have enhanced, or even entirely new, catalytic or physicalproperties. For example, the following properties are optionallymodified by inclusion of an unnatural amino acid, e.g., an unnaturalamino acid comprising a moiety where a saccharide moiety can beattached, or an unnatural amino acid that includes a saccharide moietyinto a protein: toxicity, biodistribution, structural properties,spectroscopic properties, chemical and/or photochemical properties,catalytic ability, half-life (e.g., serum half-life), ability to reactwith other molecules, e.g., covalently or noncovalently, and the like.The compositions including proteins that include at least one unnaturalamino acid, e.g., an unnatural amino acid comprising a moiety where asaccharide moiety can be attached, or an unnatural amino acid thatincludes a saccharide moiety are useful for, e.g., novel therapeutics,diagnostics, catalytic enzymes, industrial enzymes, binding proteins(e.g., antibodies), and e.g., the study of protein structure andfunction. See, e.g., Dougherty, (2000) Unnatural Amino Acids as Probesof Protein Structure and Function, Current Opinion in Chemical Biology,4:645-652.

In one aspect of the invention, a composition includes at least oneprotein with at least one, e.g., at least two, at least three, at leastfour, at least five, at least six, at least seven, at least eight, atleast nine, or at least ten or more unnatural amino acids, e.g., anunnatural amino acid comprising a moiety where a saccharide moiety canbe attached, or an unnatural amino acid that includes a saccharidemoiety, and/or which include another unnatural amino acid. The unnaturalamino acids can be the same or different, e.g., there can be 1, 2, 3, 4,5, 6, 7, 8, 9, or 10 or more different sites in the protein thatcomprise 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more different unnaturalamino acids. In another aspect, a composition includes a protein with atleast one, but fewer than all, of a particular amino acid present in theprotein substituted with the unnatural amino acid, e.g., an unnaturalamino acid comprising a moiety where a saccharide moiety can beattached, or an unnatural amino acid that includes a saccharide moiety.For a given protein with more than one unnatural amino acids, theunnatural amino acids can be identical or different (e.g., the proteincan include two or more different types of unnatural amino acids, or caninclude two of the same unnatural amino acid). For a given protein withmore than two unnatural amino acids, the unnatural amino acids can bethe same, different, or a combination of multiple unnatural amino acidsof the same kind with at least one different unnatural amino acid.

Essentially any protein (or portion thereof) that includes an unnaturalamino acid, e.g., an unnatural amino acid comprising a moiety where asaccharide moiety is attached, such as an aldehyde- or keto-derivatizedamino acid, or an unnatural amino acid that includes a saccharide moiety(and any corresponding coding nucleic acid, e.g., which includes one ormore selector codons) can be produced using the compositions and methodsherein. No attempt is made to identify the hundreds of thousands ofknown proteins, any of which can be modified to include one or moreunnatural amino acid, e.g., by tailoring any available mutation methodsto include one or more appropriate selector codon in a relevanttranslation system. Common sequence repositories for known proteinsinclude GenBank EMBL, DDBJ and the NCBI. Other repositories can easilybe identified by searching the internet.

Typically, the proteins are, e.g., at least 60%, at least 70%, at least75%, at least 80%, at least 90%, at least 95%, or at least 99% or moreidentical to any available protein (e.g., a therapeutic protein, adiagnostic protein, an industrial enzyme, or portion thereof, and thelike), and they comprise one or more unnatural amino acid. Examples oftherapeutic, diagnostic, and other proteins that can be modified tocomprise one or more unnatural amino acid, e.g., an unnatural amino acidcomprising a moiety where a saccharide moiety is attached, or anunnatural amino acid that includes a saccharide moiety, can be found,but not limited to, those in WO 2002/085923, supra. Examples oftherapeutic, diagnostic, and other proteins that can be modified tocomprise one or more unnatural amino acid that comprises an amino acid,where a saccharide moiety is linked and/or an unnatural amino acid thatincludes a saccharide moiety include, but are not limited to, e.g.,Alpha-1 antitrypsin, Angiostatin, Antihemolytic factor, antibodies(further details on antibodies are found below), Apolipoprotein,Apoprotein, Atrial natriuretic factor, Atrial natriuretic polypeptide,Atrial peptides, C—X—C chemokines (e.g., T39765, NAP-2, ENA-78, Gro-a,Gro-b, Gro-c, IP-10, GCP-2, NAP-4, SDF-1, PF4, MIG), Calcitonin, CCchemokines (e.g., Monocyte chemoattractant protein-1, Monocytechemoattractant protein-2, Monocyte chemoattractant protein-3, Monocyteinflammatory protein-1 alpha, Monocyte inflammatory protein-1 beta,RANTES, 1309, R83915, R91733, HCC1, T58847, D31065, T64262), CD40ligand, C-kit Ligand, Collagen, Colony stimulating factor (CSF),Complement factor 5a, Complement inhibitor, Complement receptor 1,cytokines, (e.g., epithelial Neutrophil Activating Peptide-78,GROα/MGSA, GROβ, GROγ, MIP-1α, MIP-1δ, MCP-1), Epidermal Growth Factor(EGF), Erythropoietin (“EPO”, representing a preferred target formodification by the incorporation of one or more unnatural amino acid),Exfoliating toxins A and B, Factor IX, Factor VII, Factor VIII, FactorX, Fibroblast Growth Factor (FGF), Fibrinogen, Fibronectin, G-CSF,GM-CSF, Glucocerebrosidase, Gonadotropin, growth factors, Hedgehogproteins (e.g., Sonic, Indian, Desert), Hemoglobin, Hepatocyte GrowthFactor (HGF), Hirudin, Human serum albumin, Insulin, Insulin-like GrowthFactor (IGF), interferons (e.g., EFN-α, IFN-β, IFN-γ), interleukins(e.g., IL-1, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10,IL-11, IL-12, etc.), Keratinocyte Growth Factor (KGF), Lactoferrin,leukemia inhibitory factor, Luciferase, Neurturin, Neutrophil inhibitoryfactor (NIF), oncostatin M, Osteogenic protein, Parathyroid hormone,PD-ECSF, PDGF, peptide hormones (e.g., Human Growth Hormone),Pleiotropin, Protein A, Protein G, Pyrogenic exotoxins A, B, and C,Relaxin, Renin, SCF, Soluble complement receptor I, Soluble I-CAM 1,Soluble interleukin receptors (IL-1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12,13, 14, 15), Soluble TNF receptor, Somatomedin, Somatostatin,Somatotropin, Streptokinase, Superantigens, i.e., Staphylococcalenterotoxins (SEA, SEB, SEC1, SEC2, SEC3, SED, SEE), Superoxidedismutase (SOD), Toxic shock syndrome toxin (TSST-1), Thymosin alpha 1,Tissue plasminogen activator, Tumor necrosis factor beta (TNF beta),Tumor necrosis factor receptor (TNFR), Tumor necrosis factor-alpha (TNFalpha), Vascular Endothelial Growth Factor (VEGEF), Urokinase and manyothers.

One class of proteins that can be made using the compositions andmethods for in vivo incorporation of an unnatural amino acid, e.g., anunnatural amino acid comprising a moiety where a saccharide moiety canbe attached, or an unnatural amino acid that includes a saccharidemoiety described herein, includes transcriptional modulators or aportion thereof. Example transcriptional modulators include genes andtranscriptional modulator proteins that modulate cell growth,differentiation, regulation, or the like. Transcriptional modulators arefound in prokaryotes, viruses, and eukaryotes, including fungi, plants,yeasts, insects, and animals, including mammals, providing a wide rangeof therapeutic targets. It will be appreciated that expression andtranscriptional activators regulate transcription by many mechanisms,e.g., by binding to receptors, stimulating a signal transductioncascade, regulating expression of transcription factors, binding topromoters and enhancers, binding to proteins that bind to promoters andenhancers, unwinding DNA, splicing pre-mRNA, polyadenylating RNA, anddegrading RNA.

One class of proteins of the invention (e.g., proteins with one or moreunnatural amino acid that comprises an amino acid, where a saccharidemoiety is linked, and/or an unnatural amino acid that includes asaccharide moiety) include expression activators such as cytokines,inflammatory molecules, growth factors, their receptors, and oncogeneproducts, e.g., interleukins (e.g., IL-1, IL-2, IL-8, etc.),interferons, FGF, IGF-I, IGF-II, FGF, PDGF, TNF, TGF-α, TGF-β, EGF, KGF,SCF/c-Kit, CD40L/CD40, VLA-4/VCAM-1, ICAM-1/LFA-1, and hyalurin/CD44;signal transduction molecules and corresponding oncogene products, e.g.,Mos, Ras, Raf, and Met; and transcriptional activators and suppressors,e.g., p53, Tat, Fos, Myc, Jun, Myb, Rel, and steroid hormone receptorssuch as those for estrogen, progesterone, testosterone, aldosterone, theLDL receptor ligand and corticosterone.

Enzymes (e.g., industrial enzymes) or portions thereof with at least oneunnatural amino acid, e.g., an unnatural amino acid comprising a moietywhere a saccharide moiety is attached, or an unnatural amino acid thatincludes a saccharide moiety, are also provided by the invention.Examples of enzymes include, but are not limited to, e.g., amidases,amino acid racemases, acylases, dehalogenases, dioxygenases,diarylpropane peroxidases, epimerases, epoxide hydrolases, esterases,isomerases, kinases, glucose isomerases, glycosidases, glycosyltransferases, haloperoxidases, monooxygenases (e.g., p450s), lipases,lignin peroxidases, nitrile hydratases, nitrilases, proteases,phosphatases, subtilisins, transaminase, and nucleases.

Many proteins that can be modified according to the invention arecommercially available (see, e.g., the Sigma BioSciences 2002 catalogueand price list), and the corresponding protein sequences and genes and,typically, many variants thereof, are well-known (see, e.g., Genbank).Any of them can be modified by the insertion of one or more unnaturalamino acid that comprises an amino acid, where a saccharide moiety islinked, or that includes an unnatural amino acid that includes asaccharide moiety according to the invention, e.g., to alter the proteinwith respect to one or more therapeutic, diagnostic or enzymaticproperties of interest. Examples of therapeutically relevant propertiesinclude serum half-life, shelf half-life, stability, immunogenicity,therapeutic activity, detectability (e.g., by the inclusion of reportergroups (e.g., labels or label binding sites) in the unnatural aminoacids, specificity, reduction of LD₅₀ or other side effects, ability toenter the body through the gastric tract (e.g., oral availability), orthe like. Examples of relevant diagnostic properties include shelfhalf-life, stability, diagnostic activity, detectability, specificity,or the like. Examples of relevant enzymatic properties include shelfhalf-life, stability, specificity, enzymatic activity, productioncapability, or the like.

A variety of other proteins can also be modified to include one or moreunnatural amino acids of the invention. For example, the invention caninclude substituting one or more natural amino acids in one or morevaccine proteins with an unnatural amino acid that comprises an aminoacid, where a saccharide moiety is linked, or by incorporating anunnatural amino acid that includes a saccharide moiety, e.g., inproteins from infectious fungi, e.g., Aspergillus, Candida species;bacteria, particularly E. coli, which serves a model for pathogenicbacteria, as well as medically important bacteria such as Staphylococci(e.g., aureus), or Streptococci (e.g., pneumoniae); protozoa such assporozoa (e.g., Plasmodia), rhizopods (e.g., Entamoeba) and flagellates(Trypanosoma, Leishmania, Trichomonas, Giardia, etc.); viruses such as(+) RNA viruses (examples include Poxviruses e.g., vaccinia;Picomaviruses, e.g. polio; Togaviruses, e.g., rubella; Flaviviruses,e.g., HCV; and Coronaviruses), (−) RNA viruses (e.g., Rhabdoviruses,e.g., VSV; Paramyxovimses, e.g., RSV; Orthomyxovimses, e.g., influenza;Bunyaviruses; and Arenaviruses), dsDNA viruses (Reoviruses, forexample), RNA to DNA viruses, i.e., Retroviruses, e.g., HIV and HTLV,and certain DNA to RNA viruses such as Hepatitis B.

Agriculturally related proteins such as insect resistance proteins(e.g., the Cry proteins), starch and lipid production enzymes, plant andinsect toxins, toxin-resistance proteins, Mycotoxin detoxificationproteins, plant growth enzymes (e.g., Ribulose 1,5-BisphosphateCarboxylase/Oxygenase, “RUBISCO”), lipoxygenase (LOX), andPhosphoenolpyruvate (PEP) carboxylase are also suitable targets formodification by incorporation of unnatural amino acids and/or saccharideadditions of invention.

In certain embodiments, the protein or polypeptide of interest (orportion thereof) in the methods and/or compositions of the invention isencoded by a nucleic acid. Typically, the nucleic acid comprises atleast one selector codon, at least two selector codons, at least threeselector codons, at least four selector codons, at least five selectorcodons, at least six selector codons, at least seven selector codons, atleast eight selector codons, at least nine selector codons, ten or moreselector codons.

Defining Polypeptides by Immunoreactivity

Because the glycopolypeptides of the invention provide a variety of newpolypeptide sequences (e.g., comprising an unnatural amino acid thatcomprises an amino acid, where a saccharide moiety can be linked, or anunnatural amino acid that includes a saccharide moiety in the case ofproteins synthesized in the translation systems herein, or, e.g., in thecase of the novel synthetases, novel sequences of standard amino acids),the glycopolypeptides also provide new structural features which can berecognized, e.g., in immunological assays. The generation of antisera,which specifically bind the polypeptides of the invention, as well asthe polypeptides which are bound by such antisera, are a feature of theinvention. The term “antibody,” as used herein, includes, but is notlimited to a polypeptide substantially encoded by an immunoglobulin geneor immunoglobulin genes, or fragments thereof which specifically bindand recognize an analyte (antigen). Examples include polyclonal,monoclonal, chimeric, and single chain antibodies, and the like.Fragments of immunoglobulins, including Fab fragments and fragmentsproduced by an expression library, including phage display, are alsoincluded in the term “antibody” as used herein. See, e.g., Paul,Fundamental Immunology, 4th Ed., 1999, Raven Press, New York, forantibody structure and terminology.

For example, the invention includes synthetase proteins thatspecifically bind to, or that are specifically immunoreactive with, anantibody or antisera generated against an immunogen comprising asynthetase amino acid sequence selected from one or more of those in thevarious sequences herein. To eliminate cross-reactivity with otherhomologues, the antibody or antisera is subtracted with availablesynthetases, such as the wild-type Methanococcus jannaschii (M.jannaschii) tyrosyl synthetase (TyrRS), or a known artificialsynthetase, such as any of those in WO 2002/085923. Where the wild-typeM. jannaschii tyrosyl synthetase (TyrRS), or previous sequence,corresponds to a nucleic acid, a polypeptide encoded by the nucleic acidis optionally generated and used for antibody/antisera subtractionpurposes.

In one typical format, the immunoassay uses polyclonal antiserum raisedagainst one or more polypeptide comprising one or more of the synthetasesequences herein, or a substantial subsequence thereof (i.e., at leastabout 30% of the full length sequence provided). The set of potentialpolypeptide immunogens derived from these sequences are collectivelyreferred to below as “the immunogenic polypeptides.” The resultingantisera is optionally selected to have low cross-reactivity against thecontrol synthetase homologues (wild type TyrRs, and/or synthetases in WO2002/085923) and any such cross-reactivity is removed, e.g., byimmunoabsorbtion, with one or more of the control synthetase homologues,prior to use of the polyclonal antiserum in the immunoassay.

In order to produce antisera for use in an immunoassay, one or more ofthe immunogenic polypeptides is produced and purified as describedherein. For example, recombinant protein can be produced in arecombinant cell. An inbred strain of mice (used in this assay becauseresults are more reproducible due to the virtual genetic identity of themice) is immunized with the immunogenic protein(s) in combination with astandard adjuvant, such as Freund's adjuvant, and a standard mouseimmunization protocol (see, e.g., Harlow and Lane (1988) Antibodies, ALaboratory Manual, Cold Spring Harbor Publications, New York, for astandard description of antibody generation, immunoassay formats andconditions that can be used to determine specific immunoreactivity.Additional references and discussion of antibodies is also found hereinand can be applied here to defining polypeptides by immunoreactivity).Alternatively, one or more synthetic or recombinant polypeptide derivedfrom the sequences disclosed herein is conjugated to a carrier proteinand used as an immunogen. Additional details on proteins, antibodies,antisera, etc. can be found in WO 2002/085923, supra.

Polyclonal sera are collected and titered against the immunogenicpolypeptide in an immunoassay, for example, a solid phase immunoassaywith one or more of the immunogenic proteins immobilized on a solidsupport. Polyclonal antisera with a titer of 106 or greater areselected, pooled and subtracted with the control synthetase polypeptidesto produce subtracted pooled titered polyclonal antisera.

The subtracted pooled titered polyclonal antisera are tested for crossreactivity against the control homologues in a comparative immunoassay.In this comparative assay, discriminatory binding conditions aredetermined for the subtracted titered polyclonal antisera which resultin at least about a 5-10 fold higher signal to noise ratio for bindingof the titered polyclonal antisera to the immunogenic synthetase ascompared to binding to the control synthetase homologues. That is, thestringency of the binding reaction is adjusted by the addition ofnon-specific competitors such as albumin or non-fat dry milk, and/or byadjusting salt conditions, temperature, and/or the like. These bindingconditions are used in subsequent assays for determining whether a testpolypeptide (a polypeptide being compared to the immunogenicpolypeptides and/or the control polypeptides) is specifically bound bythe pooled subtracted polyclonal antisera. In particular, testpolypeptides which show at least a 2-5× higher signal to noise ratiothan the control synthetase homologues under discriminatory bindingconditions, and at least about a ½ signal to noise ratio as compared tothe immunogenic polypeptide(s), shares substantial structural similaritywith the immunogenic polypeptide as compared to known synthetases, andis, therefore a polypeptide of the invention.

In another example, immunoassays in the competitive binding format areused for detection of a test polypeptide. For example, as noted,cross-reacting antibodies are removed from the pooled antisera mixtureby immunoabsorbtion with the control polypeptides. The immunogenicpolypeptide(s) are then immobilized to a solid support which is exposedto the subtracted pooled antisera. Test proteins are added to the assayto compete for binding to the pooled subtracted antisera. The ability ofthe test protein(s) to compete for binding to the pooled subtractedantisera as compared to the immobilized protein(s) is compared to theability of the immunogenic polypeptide(s) added to the assay to competefor binding (the immunogenic polypeptides compete effectively with theimmobilized immunogenic polypeptides for binding to the pooledantisera). The percent cross-reactivity for the test proteins iscalculated, using standard calculations.

In a parallel assay, the ability of the control proteins to compete forbinding to the pooled subtracted antisera is optionally determined ascompared to the ability of the immunogenic polypeptide(s) to compete forbinding to the antisera. Again, the percent cross-reactivity for thecontrol polypeptides is calculated, using standard calculations. Wherethe percent cross-reactivity is at least 5-10× as high for the testpolypeptides as compared to the control polypeptides and or where thebinding of the test polypeptides is approximately in the range of thebinding of the immunogenic polypeptides, the test polypeptides are saidto specifically bind the pooled subtracted antisera.

In general, the immunoabsorbed and pooled antisera can be used in acompetitive binding immunoassay as described herein to compare any testpolypeptide to the immunogenic and/or control polypeptide(s). In orderto make this comparison, the immunogenic, test and control polypeptidesare each assayed at a wide range of concentrations and the amount ofeach polypeptide required to inhibit 50% of the binding of thesubtracted antisera to, e.g., an immobilized control, test orimmunogenic protein is determined using standard techniques. If theamount of the test polypeptide required for binding in the competitiveassay is less than twice the amount of the immunogenic polypeptide thatis required, then the test polypeptide is said to specifically bind toan antibody generated to the immunogenic protein, provided the amount isat least about 5-10× as high as for the control polypeptide.

As an additional determination of specificity, the pooled antisera isoptionally fully immunosorbed with the immunogenic polypeptide(s)(rather than the control polypeptides) until little or no binding of theresulting immunogenic polypeptide subtracted pooled antisera to theimmunogenic polypeptide(s) used in the immunosorbtion is detectable.This fully immunosorbed antisera is then tested for reactivity with thetest polypeptide. If little or no reactivity is observed (i.e., no morethan 2× the signal to noise ratio observed for binding of the fullyimmunosorbed antisera to the immunogenic polypeptide), then the testpolypeptide is specifically bound by the antisera elicited by theimmunogenic protein.

Orthogonal tRNA and Orthogonal Aminoacyl-tRNA Synthetase Pairs

Translation systems that are suitable for making proteins that includeone or more unnatural amino acids are described in International patentapplications WO 2002/086075, entitled “METHODS AND COMPOSITION FOR THEPRODUCTION OF ORTHOGONAL tRNA-AMINOACYLtRNA SYNTHETASE PARS” and WO2002/085923, supra. Each of these applications is incorporated herein byreference in its entirety. Such translation systems generally comprisecells that include an orthogonal tRNA (O-tRNA), an orthogonal aminoacyltRNA synthetase (O-RS), and an unnatural amino acid (for example, anunnatural amino acid comprising a moiety where a saccharide moiety canbe attached, such as an aldehyde- or keto-derivatized amino acid, or anunnatural amino acid that includes a saccharide moiety), where the O-RSaminoacylates the O-tRNA with the unnatural amino acid. The cell usesthe components to incorporate the unnatural amino acid into a growingpolypeptide chain.

An orthogonal pair is composed of an O-tRNA, e.g., a suppressor tRNA, aframeshift tRNA, or the like, and an O-RS. The O-tRNA is not acylated byendogenous synthetases and is capable of decoding a selector codon, asdescribed above. The O-RS recognizes the O-tRNA, e.g., with an extendedanticodon loop, and preferentially aminoacylates the O-tRNA with anunnatural amino acid, e.g., an unnatural amino acid comprising a moietywhere a saccharide moiety can be attached, or an unnatural amino acidthat includes a saccharide moiety. The development of multipleorthogonal tRNA/synthetase pairs can allow the simultaneousincorporation of multiple unnatural amino acids using different codons.See Example 5 for exemplary O-tRNA and O-RS sequences.

The O-tRNA and the O-RS can be naturally occurring or can be derived bymutation of a naturally occurring tRNA and/or RS from a variety oforganisms, which are described under sources and hosts. In variousembodiments, the O-tRNA and O-RS are derived from at least one organism.In another embodiment, the O-tRNA is derived from a naturally occurringor mutated naturally occurring tRNA from a first organism and the O-RSis derived from naturally occurring or mutated naturally occurring RSfrom a second organism.

Specifically, these methods include: (a) generating a library of tRNAsderived from at least one tRNA from a first organism; (b) negativelyselecting the library for tRNAs that are aminoacylated by anaminoacyl-tRNA synthetase (RS) from a second organism in the absence ofa RS from the first organism, thereby providing a pool of tRNAs; (c)selecting the pool of tRNAs for members that are aminoacylated by anintroduced orthogonal RS(O-RS), thereby providing at least onerecombinant O-tRNA. The recombinant O-tRNA recognizes a selector codonand is not efficiency recognized by the RS from the second organism andis preferentially aminoacylated by the O-RS. The method also includes:(d) generating a library of mutant RSs derived from at least oneaminoacyl-tRNA synthetase (RS) from a third organism; (e) selecting thelibrary of RSs for members that preferentially aminoacylate therecombinant O-tRNA in the presence of an unnatural amino acid and anatural amino acid, thereby providing a pool of active RSs; and, (f)negatively selecting the pool for active RSs that preferentiallyaminoacylate the at least one recombinant O-tRNA in the absence of theunnatural amino acid, thereby providing the specific O-tRNA/O-RS pair,where the specific O-tRNA/O-RS pair comprises at least one recombinantO-RS that is specific for the unnatural amino acid, e.g., an unnaturalamino acid comprising a moiety where a saccharide moiety can beattached, or an unnatural amino acid that includes a saccharide moiety,and the recombinant O-tRNA.

One strategy for generating an orthogonal pair involves generatingmutant libraries from which to screen and/or select an O-tRNA or O-RS.

A second strategy for generating an orthogonal tRNA/synthetase pairinvolves importing a heterologous tRNA/synthetase pair, e.g., importinga pair from another, e.g., source organism into the host cell. Theproperties of the heterologous synthetase candidate include, e.g., thatit does not charge any host cell tRNA, and the properties of theheterologous tRNA candidate include, e.g., that it is not acylated byany host cell synthetase. In addition, the heterologous tRNA derivedfrom the heterologous tRNA is orthogonal to all host cell synthetases.

Orthogonal Aminoacyl tRNA Synthetases (O-RS)

An O-RS of the invention preferentially aminoacylates an O-tRNA with aan unnatural amino acid, e.g., an unnatural amino acid comprising amoiety where a saccharide moiety can be attached, or an unnatural aminoacid that includes a saccharide moiety, in vitro or in vivo. An O-RS ofthe invention can be provided to the translation system, e.g., a cell,or an in vivo translation system by a polypeptide that includes an O-RSand/or by a polynucleotide that encodes an O-RS or a portion thereof.For example, an O-RS comprises an amino acid sequence as set forth inSEQ ID NO.: 1-6, or a conservative variation thereof. In anotherexample, an O-RS, or a portion thereof, is encoded by a polynucleotidesequence that encodes an amino acid comprising SEQ ID NO.: 1-6, or acomplementary polynucleotide sequence thereof, or is encoded by apolynucleotide comprising a polynucleotide sequence of any one of SEQ IDNO.: 8, 9, or 10. See, e.g., Table 2 and Example 5 herein for sequencesof exemplary O-RS molecules. See also the section entitled “Nucleic Acidand Polypeptide Sequence and Variants” herein.

Methods for producing an O-RS are based on generating a pool of mutantsynthetases from the framework of a wild-type synthetase, and thenselecting for mutated RSs based on their specificity for an unnaturalamino acid having, e.g., an aldehyde- or keto-moiety or a saccharidemoiety relative to the common twenty amino acids. To isolate such asynthetase, the selection methods of the invention are: (i) sensitive,as the activity of desired synthetases from the initial rounds can below and the population small; (ii) “tunable”, since it is desirable tovary the selection stringency at different selection rounds; and, (iii)general, so that it can be used for different unnatural amino acids.

Methods to generate an orthogonal aminoacyl tRNA synthetase includemutating the synthetase, e.g., at the active site in the synthetase, atthe editing mechanism site in the synthetase, at different sites bycombining different domains of synthetases, or the like, and applying aselection process. A strategy is used, which is based on the combinationof a positive selection followed by a negative selection. In thepositive selection, suppression of the selector codon introduced at anonessential position(s) of a positive marker allows cells to surviveunder positive selection pressure. In the presence of both natural andunnatural amino acids, survivors thus encode active synthetases chargingthe orthogonal suppressor tRNA with either a natural or unnatural aminoacid. In the negative selection in the absence of the unnatural aminoacid, suppression of a selector codon introduced at a nonessentialposition(s) of a negative marker removes synthetases with natural aminoacid specificities. Survivors of the negative and positive selectionencode synthetases that aminoacylate (charge) the orthogonal suppressortRNA with unnatural amino acids only. These synthetases can then besubjected to further mutagenesis, e.g., DNA shuffling, other recursivemutagenesis methods, and/or the like.

The library of mutant RSs can be generated using various mutagenesistechniques known in the art. For example, the mutant RSs can begenerated by site-specific mutations, random point mutations, homologousrecombination, chimeric construction or the like. Chimeric libraries ofRSs are also included in the invention.

The positive selection can be based on suppression of a selector codonin a positive selection marker comprising a selector codon, e.g., anamber stop codon, in the selection marker gene. The antibiotic or otherselective agent can be applied as the positive selection pressure. Inaddition, the selection marker can be used as both a positive marker andnegative marker, as describe herein, in the presence and absence ofunnatural amino acid. Optionally, the selection marker gene comprising aselector codon is used for the positive selection and a negativeselection marker, e.g., a toxic marker, such as a barnase genecomprising at least one or more selector codons, is used for thenegative selection.

The positive selection can also be based on suppression of a selectorcodon at a nonessential position in the β-lactamase gene, renderingcells ampicillin resistant; and a negative selection using theribonuclease barnase as the negative marker is used. In contrast toβ-lactamase, which is secreted into the periplasm, a chloramphenicolacetyltransferase (CAT) gene can also be used, which localizes in thecytoplasm; moreover, ampicillin is bactericidal, while chloramphenicolis bacteriostatic.

Once the synthetases are subject to the positive and negativeselection/screening strategy, these synthetases can then be subjected tofurther mutagenesis. For example, a nucleic acid that encodes the O-RScan be isolated; a set of polynucleotides that encode mutated O-RSs(e.g., by random mutagenesis, site-specific mutagenesis, recombinationor any combination thereof) can be generated from the nucleic acid; and,these individual steps or a combination of these steps can be repeateduntil a mutated O-RS is obtained that preferentially aminoacylates theO-tRNA with the unnatural amino acid, e.g., an unnatural amino acidcomprising a moiety where a saccharide moiety can be attached, or anunnatural amino acid that includes a saccharide moiety. In one aspect ofthe invention, the steps are performed multiple times, e.g., at leasttwo times. Optionally, the concentration of the selection agent isvaried.

Additional levels of selection/screening stringency can also be used inthe methods of the invention, for producing O-tRNA, O-RS, or pairsthereof. The selection or screening stringency can be varied on one orboth steps of the method to produce an O-RS. This could include, e.g.,varying the amount of selection/screening agent that is used, etc.Additional rounds of positive and/or negative selections can also beperformed. Selecting or screening can also comprise one or more of achange in amino acid permeability, a change in translation efficiency, achange in translational fidelity, etc. Typically, the one or more changeis based upon a mutation in one or more gene in an organism in which anorthogonal tRNA-tRNA synthetase pair is used to produce protein.

Additional details for producing O-RS, for altering the substratespecificity of the synthetase, and other examples of O-RSs can be foundin WO 2002/086075, supra.

Orthogonal tRNA (O-tRNAS)

An orthogonal tRNA (O-tRNA) of the invention mediates incorporation ofan unnatural amino acid, e.g., an unnatural amino acid comprising amoiety where a saccharide moiety can be attached, such as an aldehyde-or keto-derivatized amino acid, or an unnatural amino acid that includesa saccharide moiety, into a protein that is encoded by a polynucleotidethat comprises a selector codon that is recognized by the O-tRNA, e.g.,in vivo or in vitro.

An example of O-tRNAs of the invention is SEQ ID NO.: 7. See Table 2 andExample 5, herein, for sequences of exemplary O-tRNA and O-RS molecules.See also the section entitled “Nucleic Acid and Polypeptide Sequence andVariants” herein. In the tRNA molecule, Thymine (T) is replace withUracil (U). Additional modifications to the bases can also be present.The invention also includes conservative variations of O-tRNA. Forexample, conservative variations of O-tRNA include those molecules thatfunction like the O-tRNA of SEQ ID NO.: 7 and maintain the tRNA L-shapedstructure, but do not have the same sequence (and are other than wildtype tRNA molecules). See also the section herein entitled “Nucleicacids and Polypeptides Sequence and Variants.”

Methods for producing a recombinant orthogonal tRNA (O-tRNA) is providedin International patent application WO 2002/086075, supra.

For example, to improve the orthogonality of a tRNA while preserving itsaffinity toward a desired RS, the methods include a combination ofnegative and positive selections with a mutant suppressor tRNA libraryin the absence and presence of the cognate synthetase, respectively. Inthe negative selection, a selector codon(s) is introduced in a markergene, e.g., a toxic gene, such as barnase, at a nonessential position.When a member of the mutated tRNA library, e.g., derived fromMethanococcus jannaschii, is aminoacylated by endogenous host, e.g.,Escherichia coli synthetases (i.e., it is not orthogonal to the host,e.g., Escherichia coli synthetases), the selector codon, e.g., an ambercodon, is suppressed and the toxic gene product produced leads to celldeath. Cells harboring orthogonal tRNAs or non-functional tRNAs survive.Survivors are then subjected to a positive selection in which a selectorcodon, e.g., an amber codon, is placed in a positive marker gene, e.g.,a drug resistance gene, such a β-lactamase gene. These cells alsocontain an expression vector with a cognate RS. These cells are grown inthe presence of a selection agent, e.g., ampicillin. tRNAs are thenselected for their ability to be aminoacylated by the coexpressedcognate synthetase and to insert an amino acid in response to thisselector codon. Cells harboring non-functional tRNAs, or tRNAs thatcannot be recognized by the synthetase of interest are sensitive to theantibiotic. Therefore, tRNAs that: (i) are not substrates for endogenoushost, e.g., Escherichia coli, synthetases; (ii) can be aminoacylated bythe synthetase of interest; and (iii) are functional in translationsurvive both selections.

Libraries of mutated tRNA are constructed. Mutations can be introducedat a specific position(s), e.g., at a nonconservative position(s), or ata conservative position, at a randomized position(s), or a combinationof both in a desired loop of a tRNA, e.g., an anticodon loop, (D arm, Vloop, TψC arm) or a combination of loops or all loops. Chimericlibraries of tRNA are also included in the invention. It should be notedthat libraries of tRNA synthetases from various organism (e.g.,microorganisms such as eubacteria or archaebacteria) such as librariesthat comprise natural diversity (see, e.g., U.S. Pat. No. 6,238,884 toShort et al; U.S. Pat. No. 5,756,316 to Schallenberger et al; U.S. Pat.No. 5,783,431 to Petersen et al; U.S. Pat. No. 5,824,485 to Thompson etal; U.S. Pat. No. 5,958,672 to Short et al), are optionally constructedand screened for orthogonal pairs.

Additional mutations can be introduced at a specific position(s), e.g.,at a nonconservative position(s), or at a conservative position, at arandomized position(s), or a combination of both in a desired loop orregion of a tRNA, e.g., an anticodon loop, the acceptor stem, D arm orloop, variable loop, TψC arm or loop, other regions of the tRNAmolecule, or a combination thereof. Typically, mutations in a tRNAinclude mutating the anticodon loop of each member of the library ofmutant tRNAs to allow recognition of a selector codon. The method canfurther include adding an additional sequence (CCA) to 3′ terminus ofthe O-tRNA. Typically, an O-tRNA possesses an improvement oforthogonality for a desired organism compared to the starting material,e.g., the plurality of tRNA sequences, while preserving its affinitytowards a desired RS.

For example, in the negative selection, a selector codon(s) isintroduced into polynucleotide that encodes a negative selection marker,e.g., an enzyme that confers antibiotic resistance, e.g., β-lactamase,an enzyme that confers a detectable product, e.g., β-galactosidase,chloramphenicol acetyltransferase (CAT), e.g., a toxic product, such asbarnase, at a nonessential position (e.g., still producing a functionalbarnase), etc. Screening/selection is optionally done by growing thepopulation of cells in the presence of a selective agent (e.g., anantibiotic, such as ampicillin). In one embodiment, the concentration ofthe selection agent is varied.

For example, to measure the activity of suppressor tRNAs, a selectionsystem is used that is based on the in vivo suppression of selectorcodon, e.g., nonsense or frameshift mutations introduced into apolynucleotide that encodes a negative selection marker, e.g., a genefor β-lactamase (bla). For example, polynucleotide variants, e.g., blavariants, with a selector codon at position a certain position, areconstructed. Cells, e.g., bacteria, are transformed with thesepolynucleotides. In the case of an orthogonal tRNA, which cannot beefficiently charged by endogenous E. coli synthetases, antibioticresistance, e.g., ampicillin resistance, should be about or less thanthat for a bacteria transformed with no plasmid. If the tRNA is notorthogonal, or if a heterologous synthetase capable of charging the tRNAis co-expressed in the system, a higher level of antibiotic, e.g.,ampicillin, resistance is be observed. Cells, e.g., bacteria, are chosenthat are unable to grow on LB agar plates with antibiotic concentrationsabout equal to cells transformed with no plasmids.

In the case of a toxic product (e.g., ribonuclease barnase), when amember of the plurality of potential tRNAs is aminoacylated byendogenous host, e.g., Escherichia coli synthetases (i.e., it is notorthogonal to the host, e.g., Escherichia coli synthetases), theselector codon is suppressed and the toxic polynucleotide productproduced leads to cell death. Cells harboring orthogonal tRNAs ornon-functional tRNAs survive. Optionally, the ribonuclease barnase genecan include two or more amber codons. The surviving cells can beselected, e.g., by using a comparison ratio cell density assay.

In one embodiment, the pool of tRNAs that are orthogonal to a desiredorganism are subjected to a positive selection in which a selector codonis placed in a positive selection marker, e.g., encoded by a drugresistance gene, such a β-lactamase gene. The positive selection isperformed on a cell comprising a polynucleotide encoding or comprising amember of the pool of tRNAs that are orthogonal to the cell, apolynucleotide encoding a positive selection marker, and apolynucleotide encoding cognate RS. In certain embodiments, the secondpopulation of cells comprises cells that were not eliminated by thenegative selection. The polynucleotides are expressed in the cell andthe cell is grown in the presence of a selection agent, e.g.,ampicillin. tRNAs are then selected for their ability to beaminoacylated by the coexpressed cognate synthetase and to insert anamino acid in response to this selector codon. Typically, these cellsshow an enhancement in suppression efficiency compared to cellsharboring non-functional tRNAs, or tRNAs that cannot efficiently berecognized by the synthetase of interest. The cell harboring thenon-functional or tRNAs that are not efficiently recognized by thesynthetase of interest are sensitive to the antibiotic. Therefore, tRNAsthat: (i) are not substrates for an endogenous host, e.g., Escherichiacoli, synthetases; (ii) can be aminoacylated by the synthetase ofinterest; and (iii) are functional in translation survive bothselections.

The stringency of the selection, e.g., the positive selection, thenegative selection or both the positive and negative selection, in theabove described-methods, optionally includes varying the selectionstringency. For example, because barnase is an extremely toxic protein,the stringency of the negative selection can be controlled byintroducing different numbers of selector codons into the barnase geneand/or by using an inducible promoter. In another example, theconcentration of the selection or screening agent is varied (e.g.,ampicillin concentration). In one aspect of the invention, thestringency is varied because the desired activity can be low duringearly rounds of screening. Thus, less stringent selection criteria areapplied in early rounds and more stringent criteria are applied in laterrounds of selection. In certain embodiments, the negative selection, thepositive selection, or both the negative and positive selection, can berepeated multiple times. Multiple different negative selection markers,positive selection markers, or both negative and positive selectionmarkers can be used. In certain embodiments, the positive and negativeselection marker can be the same.

Other types of selections can be used in the invention for generating,e.g., O-RS, O-tRNA, and O-tRNA/O-RS pairs that utilize, e.g., anunnatural amino acid comprising a moiety where a saccharide moiety canbe attached, such as an aldehyde- or keto-derivatized amino acid, or anunnatural amino acid that includes a saccharide moiety. For example, thepositive selection step, the negative selection step or both thepositive and negative selection steps can include using a reporter,wherein the reporter is detected by fluorescence-activated cell sorting(FACS). For example, a positive selection can be done first with apositive selection marker, e.g., a chloramphenicol acetyltransferase(CAT) gene, where the CAT gene comprises a selector codon, e.g., anamber stop codon, in the CAT gene, which followed by a negativeselection screen, that is based on the inability to suppress a selectorcodon(s), e.g., two or more codons, at positions within a negativemarker, e.g., a T7 RNA polymerase gene, which effects transcription ofanother gene, e.g., GFP. In one embodiment, the positive selectionmarker and the negative selection marker can be found on the samevector, e.g., plasmid. Expression of the negative marker drivesexpression of the reporter, e.g., green fluorescent protein (GFP). Thestringency of the selection and screen can be varied, e.g., theintensity of the light need to fluorescence the reporter can be varied.In another embodiment, a positive selection can be done with a reporteras a positive selection marker, which is screened by FACs, followed by anegative selection screen, that is based on the inability to suppress aselector codon(s), e.g., two or more, at positions within a negativemarker, e.g., barnase gene. See also, e.g., Example 4, herein.

Optionally, the reporter is displayed on a cell surface, on a phagedisplay or the like. Cell-surface display, e.g., the OmpA-basedcell-surface display system, relies on the expression of a particularepitope, e.g., a poliovirus C3 peptide fused to an outer membrane porinOmpA, on the surface of the Escherichia coli cell. The epitope isdisplayed on the cell surface only when a selector codon in the proteinmessage is suppressed during translation. The displayed peptide thencontains the amino acid recognized by one of the mutant aminoacyl-tRNAsynthetases in the library, and the cell containing the correspondingsynthetase gene can be isolated with antibodies raised against peptidescontaining specific unnatural amino acids. The OmpA-based cell-surfacedisplay system was developed and optimized by Georgiou et al. as analternative to phage display. See Francisco, J. A., Campbell, R.,Iverson, B. L. & Georgoiu, G. Production and fluorescence-activated cellsorting of Escherichia coli expressing a functional antibody fragment onthe external surface. Proc Natl Acad Sci USA. 90:104448 (1993).

The selection steps can also be carried out in vitro. The selectedcomponent, e.g., synthetase and/or tRNA, can then be introduced into acell for use in in vivo incorporation of an unnatural amino acid.

Additional methods for producing a recombinant orthogonal tRNA can befound, e.g., in International patent applications WO 2002/086075, supra.See also Forster et al., (2003) Programming peptidomimetic synthetasesby translating genetic codes designed de novo PNAS 100(11):6353-6357;and, Feng et al., (2003), Expanding tRNA recognition of a tRNAsynthetase by a single amino acid change, PNAS 100(10): 5676-5681.

Source and Host Organisms

The translational components to produce glycoproteins of the inventionare typically derived from non-eukaryotic organisms. For example, theorthogonal O-tRNA can be derived from a non-eukaryotic organism (or acombination of organisms), e.g., an archaebacterium, such asMethanococcus jannaschii, Methanobacterium thermoautotrophicum,Halobacterium such as Haloferax volcanii and Halobacterium speciesNRC-1, Archaeoglobus fulgidus, Pyrococcus furiosus, Pyrococcushorikoshii, Aeuropyrum pernix, Methanococcus maripaludis, Methanopyruskandleri, Methanosarcina mazei (Mm), Pyrobaculum aerophilum, Pyrococcusabyssi, Sulfolobus solfataricus (Ss), Sulfolobus tokodaii, Thermoplasmaacidophilum, Thermoplasma volcanium, or the like, or a eubacterium, suchas Escherichia coli, Thermus thermophilus, Bacillus stearothermphilus,or the like, while the orthogonal O-RS can be derived from anon-eukaryotic organism (or a combination of organisms), e.g., anarchaebacterium, such as Methanococcus jannaschii, Methanobacteriumthermoautotrophicum, Halobacterium such as Haloferax volcanii andHalobacterium species NRC-1, Archaeoglobus fulgidus, Pyrococcusfuriosus, Pyrococcus horikoshii, Aeuropyrum pernix, Methanococcusmaripaludis, Methanopyrus kandleri, Methanosarcina mazei, Pyrobaculumaerophilum, Pyrococcus abyssi, Sulfolobus solfataricus, Sulfolobustokodaii, Thermoplasma acidophilum, Thermoplasma volcanium, or the like,or a eubacterium, such as Escherichia coli, Thermus thermophilus,Bacillus stearothermphilus, or the like. In one embodiment, eukaryoticsources, e.g., plants (e.g., complex plants such as monocots, ordicots), algae, protists, fungi, yeasts, animals (e.g., mammals,insects, arthropods, etc.), or the like, can also be used as sources ofO-tRNAs and O-RSs.

The individual components of an O-tRNA/O-RS pair can be derived from thesame organism or different organisms. The orthogonal tRNA-RS pair can beused in a variety of host organisms, e.g., a second organism. In oneembodiment, the O-tRNA/O-RS pair is from the same organism.Alternatively, the O-tRNA and the O-RS of the O-tRNA/O-RS pair are fromdifferent organisms.

Selector Codons

Selector codons of the invention expand the genetic codon framework ofprotein biosynthetic machinery for the incorporation of an unnaturalamino acid, e.g., an unnatural amino acid comprising a moiety where asaccharide moiety can be attached, or an unnatural amino acid thatincludes a saccharide moiety. For example, a selector codon includes,e.g., a unique three base codon, a nonsense codon, such as a stop codon,e.g., an amber codon, or an opal codon, an unnatural codon, at least afour base codon, a rare codon, or the like. A number of selector codonscan be introduced into a desired gene, e.g., one or more, two or more,more than three, etc.

The 64 genetic codons code for 20 amino acids and three stop codons.Because only one stop codon is needed for translational termination, theother two can in principle be used to encode nonproteinogenic aminoacids. The amber stop codon, UAG, has been successfully used in in vitrobiosynthetic system and in Xenopus oocytes to direct the incorporationof unnatural amino acids. Among the three stop codons, UAG is the leastused stop codon in Escherichia coli. Some Escherichia coli strainscontain natural suppressor tRNAs, which recognize UAG and insert anatural amino acid. In addition, these amber suppressor tRNAs have beenused in conventional protein mutagenesis. In certain embodiments of theinvention, other stop codons are used in the invention.

In one embodiment, the methods involve the use of a selector codon thatis a stop codon for the incorporation of unnatural amino acids in vivo.For example, an O-tRNA is generated that recognizes the stop codon,e.g., UAG, and is aminoacylated by an O-RS with a desired unnaturalamino acid. This O-tRNA is not recognized by the naturally occurringaminoacyl-tRNA synthetases. Conventional site-directed mutagenesis canbe used to introduce the stop codon, e.g., TAG, at the site of interestin the protein gene. See, e.g., Sayers, J. R., Schmidt, W. Eckstein, F.5′,3′ Exonuclease in phosphorothioate-based oligonucleotide-directedmutagenesis. Nucleic Acids Res, 791-802 (1988). When the O-RS, O-tRNAand the mutant gene are combined in vivo, the unnatural amino acid isincorporated in response to the UAG codon to give a protein containingthe unnatural amino acid at the specified position.

The incorporation of unnatural amino acids in vivo can be done withoutsignificant perturbation of the host, e.g., Escherichia coli. Forexample, in non-eukaryotic cells, such as Escherichia coli, because thesuppression efficiency for the UAG codon depends upon the competitionbetween the O-tRNA, e.g., the amber suppressor tRNA, and the releasefactor 1 (RF1) (which binds to the UAG codon and initiates release ofthe growing peptide from the ribosome), the suppression efficiency canbe modulated by, e.g., either increasing the expression level of O-tRNA,e.g., the suppressor tRNA, or using an RF1 deficient strain.

Unnatural amino acids, e.g., unnatural amino acids comprising a moietywhere a saccharide moiety can be attached, such as an aldehyde- orketo-derivatized amino acids or unnatural amino acids that includes asaccharide moiety, can also be encoded with rare codons. For example,when the arginine concentration in an in vitro protein synthesisreaction is reduced, the rare arginine codon, AGG, has proven to beefficient for insertion of Ala by a synthetic tRNA acylated withalanine. See, e.g., Ma et al., Biochemistry, 32:7939 (1993). In thiscase, the synthetic tRNA competes with the naturally occurring tRNAArg,which exists as a minor species in Escherichia coli. Some organisms donot use all triplet codons. An unassigned codon AGA in Micrococcusluteus has been utilized for insertion of amino acids in an in vitrotranscription/translation extract. See, e.g., Kowal and Oliver, Nucl.Acid. Res. 25:4685 (1997). Components of the invention can be generatedto use these rare codons in vivo.

Selector codons also comprise four or more base codons, such as, four,five, six or more base codons. Examples of four base codons include,e.g., AGGA, CUAG, UAGA, CCCU and the like. Examples of five base codonsinclude, e.g., AGGAC, CCCCU, CCCUC, CUAGA, CUACU, UAGGC and the like.For example, in the presence of mutated O-tRNAs, e.g., a specialframeshift suppressor tRNAs, with anticodon loops, e.g., with at least8-10 nt anticodon loops, the four or more base codon is read as singleamino acid. In other embodiments, the anticodon loops can decode, e.g.,at least a four-base codon, at least a five-base codon, or at least asix-base codon or more. Since there are 256 possible four-base codons,multiple unnatural amino acids can be encoded in the same cell using thefour or more base codon. See Anderson et al., Exploring the Limits ofCodon and Anticodon Size, Chemistry and Biology, Vol. 9, 237-244 (2002);and, Magliery, Expanding the Genetic Code: Selection of EfficientSuppressors of Four-base Codons and Identification of “Shifty” Four-baseCodons with a Library Approach in Escherichia coli, J. Mol. Biol. 307:755-769 (2001).

Methods of the invention include using extended codons based onframeshift suppression. Four or more base codons can insert, e.g., oneor multiple unnatural amino acids into the same protein. For example,four-base codons have been used to incorporate unnatural amino acidsinto proteins using in vitro biosynthetic methods. See, e.g., Ma et al.,Biochemistry, 1993, 32, 7939 (1993); and Hohsaka et al., J. Am. Chem.Soc., 121:34 (1999). CGGG and AGGU were used to simultaneouslyincorporate 2-naphthylalanine and an NBD derivative of lysine intostreptavidin in vitro with two chemically acylated frameshift suppressortRNAs. See, e.g., Hohsaka et al., J. Am. Chem. Soc., 121:12194 (1999).In an in vivo study, Moore et al. examined the ability of tRNA^(Leu)derivatives with NCUA anticodons to suppress UAGN codons (N can be U, A,G, or C), and found that the quadruplet UAGA can be decoded by atRNA^(Leu) with a UCUA anticodon with an efficiency of 13 to 26% withlittle decoding in the 0 or −1 frame. See Moore et al., J. Mol. Biol.298:195 (2000). In one embodiment, extended codons based on rare codonsor nonsense codons can be used in invention, which can reduce missensereadthrough and frameshift suppression at other unwanted sites.

A translational bypassing system can also be used to incorporate anunnatural amino acid, e.g., an unnatural amino acid comprising a moietywhere a saccharide moiety can be attached, or an unnatural amino acidthat includes a saccharide moiety, in a desired polypeptide. In atranslational bypassing system, a large sequence is inserted into a genebut is not translated into protein. The sequence contains a structurethat serves as a cue to induce the ribosome to hop over the sequence andresume translation downstream of the insertion.

Alternatively, or in combination with others methods described above toincorporate an unnatural amino acid, e.g., an unnatural amino acidcomprising a moiety where a saccharide moiety can be attached, or anunnatural amino acid that includes a saccharide moiety, in apolypeptide, a trans-translation system can be used. This systeminvolves a molecule called tmRNA present in Escherichia coli. This RNAmolecule is structurally related to an alanyl tRNA and is aminoacylatedby the alanyl synthetase. The difference between tmRNA and tRNA is thatthe anticodon loop is replaced with a special large sequence. Thissequence allows the ribosome to resume translation on sequences thathave stalled using an open reading frame encoded within the tmRNA astemplate. In the invention, an orthogonal tmRNA can be generated that ispreferentially aminoacylated with an orthogonal synthetase and loadedwith an unnatural amino acid. By transcribing a gene using the system,the ribosome stalls at a specific site; the unnatural amino acid isintroduced at that site, then translation resumes, using the sequenceencoded within the orthogonal tmRNA.

For a given system, a selector codon can also include one of the naturalthree base codons, where the endogenous system does not use (or rarelyuses) the natural base codon. For example, this includes a system thatis lacking a tRNA that recognizes the natural three base codon, and/or asystem where the three base codon is a rare codon.

Selector codons optionally include unnatural base pairs. These unnaturalbase pairs further expand the existing genetic alphabet. One extra basepair increases the number of triplet codons from 64 to 125. Propertiesof third base pairs include stable and selective base pairing, efficientenzymatic incorporation into DNA with high fidelity by a polymerase, andthe efficient continued primer extension after synthesis of the nascentunnatural base pair. Descriptions of unnatural base pairs which can beadapted for methods and compositions include, e.g., Hirao, et al., Anunnatural base pairfor incorporating amino acid analogues into protein,Nature Biotechnology, 20:177-182 (2002). Other relevant publications arelisted below.

For in vivo usage, the unnatural nucleoside is membrane permeable and isphosphorylated to form the corresponding triphosphate. In addition, theincreased genetic information is stable and not destroyed by cellularenzymes. Previous efforts by Benner and others took advantage ofhydrogen bonding patterns that are different from those in canonicalWatson-Crick pairs, the most noteworthy example of which is theiso-C:iso-G pair. See, e.g., Switzer et al., J. Am. Chem. Soc., 111:8322(1989); and Piccirilli et al., Nature, 1990, 343:33 (1990); Kool, Curr.Opin. Chem. Biol., 4:602 (2000). These bases in general mispair to somedegree with natural bases and cannot be enzymatically replicated. Kooland co-workers demonstrated that hydrophobic packing interactionsbetween bases can replace hydrogen bonding to drive the formation ofbase pair. See Kool, Curr. Opin. Chem. Biol., 4:602 (2000); and Guckianand Kool, Angew. Chem. Int. Ed. Engl. 36, 2825 (1998). In an effort todevelop an unnatural base pair satisfying all the above requirements,Schultz, Romesberg and co-workers have systematically synthesized andstudied a series of unnatural hydrophobic bases. A PICS:PICS self-pairis found to be more stable than natural base pairs, and can beefficiently incorporated into DNA by Klenow fragment of Escherichia coliDNA polymerase I (KF). See, e.g., McMinn et al., J. Am. Chem. Soc.,121:11586 (1999); and Ogawa et al., J. Am. Chem. Soc., 122:3274 (2000).A 3MN:3MN self-pair can be synthesized by KF with efficiency andselectivity sufficient for biological function. See, e.g., Ogawa et al.,J. Am. Chem. Soc., 122:8803 (2000). However, both bases act as a chainterminator for further replication. A mutant DNA polymerase has beenrecently evolved that can be used to replicate the PICS self pair. Inaddition, a 7AI self pair can be replicated. See, e.g., Tae et al., J.Am. Chem. Soc. 123:7439 (2001). A novel metallobase pair, Dipic:Py, hasalso been developed, which forms a stable pair upon binding Cu(II). SeeMeggers et al., J. Am. Chem. Soc. 122:10714 (2000). Because extendedcodons and unnatural codons are intrinsically orthogonal to naturalcodons, the methods of the invention can take advantage of this propertyto generate orthogonal tRNAs for them.

Unnatural Amino Acids

As used herein an unnatural amino acid refers to any amino acid,modified amino acid, or amino acid analogue other than selenocysteineand/or pyrrolysine and the following twenty genetically encodedalpha-amino acids: alanine, arginine, asparagine, aspartic acid,cysteine, glutamine, glutamic acid, glycine, histidine, isoleucine,leucine, lysine, methionine, phenylalanine, proline, serine, threonine,tryptophan, tyrosine, valine. The generic structure of an alpha-aminoacid is illustrated by Formula I:

An unnatural amino acid is typically any structure having Formula Iwherein the R group is any substituent other than one used in the twentynatural amino acids. See, e.g., Biochemistry by L. Stryer, 3^(rd) ed.1988, Freeman and Company, New York, for structures of the twentynatural amino acids. Note that, the unnatural amino acids of theinvention can be naturally occurring compounds other than the twentyalpha-amino acids above.

Because the unnatural amino acids of the invention optionally differfrom the natural amino acids in side chain only, the unnatural aminoacids can typically form amide bonds with other amino acids, e.g.,natural or unnatural, in the same manner in which they are formed innaturally occurring proteins. However, the unnatural amino acids haveside chain groups that distinguish them from the natural amino acids.

Of particular interest for making glycoproteins of the invention areunnatural amino acids in which R in Formula I includes a moiety that canreact with a reactive group that is attached to a saccharide moiety tolink the saccharide moiety to a protein that includes the unnaturalamino acid. Suitable R groups include, for example, keto-, azido-,hydroxyl-, hydrazine, cyano-, halo-, aminooxy-, alkenyl, alkynyl,carbonyl, ether, thiol, seleno-, sulfonyl-, borate, boronate, phospho,phosphono, phosphine, heterocyclic, enone, imine, aldehyde, ester,thioacid, thioester, hindered ester, hydroxylamine, amine, and the like,or any combination thereof. In some embodiments, the unnatural aminoacids have a photoactivatable cross-linker.

In addition to unnatural amino acids that contain novel side chains,unnatural amino acids also optionally comprise modified backbonestructures, e.g., as illustrated by the structures of Formula II andIII:

wherein Z typically comprises OH, NH₂, SH, NH—R′, or S—R′; X and Y,which can be the same or different, typically comprise S or O, and R andR′, which are optionally the same or different, are typically selectedfrom the same list of constituents for the R group described above forthe unnatural amino acids having Formula I as well as hydrogen. Forexample, unnatural amino acids of the invention optionally comprisesubstitutions in the amino or carboxyl group as illustrated by FormulasII and III. Unnatural amino acids of this type include, but are notlimited to, α-hydroxy acids, α-thioacids α-aminothiocarboxylates, e.g.,with side chains corresponding to the common twenty natural amino acidsor unnatural side chains. In addition, substitutions at the α-carbonoptionally include L, D, or α-α-disubstituted amino acids such asD-glutamate, D-alanine, D-methyl-O-tyrosine, aminobutyric acid, and thelike. Other structural alternatives include cyclic amino acids, such asproline analogues as well as 3, 4, 6, 7, 8, and 9 membered ring prolineanalogues, β and γ amino acids such as substituted β-alanine and γ-aminobutyric acid.

For example, many unnatural amino acids are based on natural aminoacids, such as tyrosine, glutamine, phenylalanine, and the like.Tyrosine analogs include para-substituted tyrosines, ortho-substitutedtyrosines, and meta substituted tyrosines, wherein the substitutedtyrosine comprises an acetyl group, a benzoyl group, an amino group, ahydrazine, an hydroxyamine, a thiol group, a carboxy group, an isopropylgroup, a methyl group, a C₆-C₂₀ straight chain or branched hydrocarbon,a saturated or unsaturated hydrocarbon, an O-methyl group, a polyethergroup, a nitro group, or the like. In addition, multiply substitutedaryl rings are also contemplated. Glutamine analogs of the inventioninclude, but are not limited to, α-hydroxy derivatives, γ-substitutedderivatives, cyclic derivatives, and amide substituted glutaminederivatives. Example phenylalanine analogs include, but are not limitedto, meta-substituted, ortho-substituted, and/or para-substitutedphenylalanines, wherein the substituent comprises a hydroxy group, amethoxy group, a methyl group, an allyl group, an aldehyde or ketogroup, or the like.

Specific examples of unnatural amino acids include, but are not limitedto, p-acetyl-L-phenylalanine, O-methyl-L-tyrosine, anL-3-(2-naphthyl)alanine, a 3-methyl-phenylalanine, anO-4-allyl-L-tyrosine, a 4-propyl-L-tyrosine, atri-O-acetyl-GlcNAcβ-serine, β-O-GlcNAc-L-serine, atri-O-acetyl-GalNAc-α-threonine, an α-GalNAc-L-threonine, an L-Dopa, afluorinated phenylalanine, an isopropyl-L-phenylalanine, ap-azido-L-phenylalanine, a p-acyl-L-phenylalanine, ap-benzoyl-L-phenylalanine, an L-phosphoserine, a phosphonoserine, aphosphonotyrosine, a p-iodo-phenylalanine, a p-bromophenylalanine, ap-amino-L-phenylalanine, an isopropyl-L-phenylalanine, those listedbelow, or elsewhere herein, and the like. The structures of a variety ofunnatural amino acids are provided in, for example, FIGS. 17, 18, 19,26, and 29 of WO 2002/085923.

Unnatural amino acids suitable for use in the methods of the inventionalso include those that have a saccharide moiety attached to the aminoacid side chain. In one embodiment, an unnatural amino acid with asaccharide moiety includes a serine or threonine amino acid with a Man,GalNAc, Glc, Fuc, or Gal moiety. Examples of unnatural amino acids thatinclude a saccharide moiety include, but are not limited to, e.g., atri-O-acetyl-GlcNAcβ-serine, a β-O-GlcNAc-L-serine, atri-O-acetyl-GalNAc-α-threonine, an α-GalNAc-L-threonine, anO-Man-L-serine, a tetra-acetyl-O-Man-L-serine, an O-GalNAc-L-serine, atri-acetyl-O-GalNAc-L-serine, a Glc-L-serine, atetraacetyl-Glc-L-serine, a fuc-L-serine, a tri-acetyl-fuc-L-serine, anO-Gal-L-serine, a tetra-acetyl-O-Gal-L-serine, abeta-O-GlcNAc-L-threonine, a tri-acetyl-beta-GlcNAc-L-threonine, anO-Man-L-threonine, a tetra-acetyl-O-Man-L-threonine, anO-GalNAc-L-threonine, a tri-acetyl-O-GalNAc-L-threonine, aGlc-L-threonine, a tetraacetyl-Glc-L-threonine, a fuc-L-threonine, atri-acetyl-fuc-L-threonine, an O-Gal-L-threonine, atetra-acetyl-O-Gal-L-serine, and the like. The invention includesunprotected and acetylated forms of the above. See also WO2003/031464A2, entitled “Remodeling and Glycoconjugation of Peptides”;and, U.S. Pat. No. 6,331,418, entitled “Saccharide Compositions, Methodsand Apparatus for their synthesis.”

Chemical Synthesis of Unnatural Amino Acids

Many of the unnatural amino acids provided above are commerciallyavailable, e.g., from Sigma (USA) or Aldrich (Milwaukee, Wis., USA).Those that are not commercially available are optionally synthesized asprovided in the examples below or using standard methods known to thoseof skill in the art. For organic synthesis techniques, see, e.g.,Organic Chemistry by Fessendon and Fessendon, (1982, Second Edition,Willard Grant Press, Boston Mass.); Advanced Organic Chemistry by March(Third Edition, 1985, Wiley and Sons, New York); and Advanced OrganicChemistry by Carey and Sundberg (Third Edition, Parts A and B, 1990,Plenum Press, New York). See also WO 2002/085923 for additionalsynthesis of unnatural amino acids.

For example, meta-substituted phenylalanines are synthesized in aprocedure as outlined in WO 2002/085923 (see, e.g., FIG. 14 of thepublication). Typically, NBS (N-bromosuccinimide) is added to ameta-substituted methylbenzene compound to give a meta-substitutedbenzyl bromide, which is then reacted with a malonate compound to givethe meta substituted phenylalanine. Typical substituents used for themeta position include, but are not limited to, ketones, methoxy groups,alkyls, acetyls, and the like. For example, 3-acetyl-phenylalanine ismade by reacting NBS with a solution of 3-methylacetophenone. For moredetails see the examples below. A similar synthesis is used to produce a3-methoxy phenylalanine. The R group on the meta position of the benzylbromide in that case is —OCH₃. See, e.g., Matsoukas et al., J. Med.Chem. 1995, 38, 4660-4669.

In some embodiments, the design of unnatural amino acids is biased byknown information about the active sites of synthetases, e.g.,orthogonal tRNA synthetases used to aminoacylate an orthogonal tRNA. Forexample, three classes of glutamine analogs are provided, includingderivatives substituted at the nitrogen of amide (1), a methyl group atthe γ-position (2), and a N-C^(γ)-cyclic derivative (3). Based upon thex-ray crystal structure of E. coli GlnRS, in which the key binding siteresidues are homologous to yeast GlnRS, the analogs were designed tocomplement an array of side chain mutations of residues within a 10 Åshell of the side chain of glutamine, e.g., a mutation of the activesite Phe233 to a small hydrophobic amino acid might be complemented byincreased steric bulk at the C^(γ) position of Gln.

For example, N-phthaloyl-L-glutamic 1,5-anhydride (compound number 4 inFIG. 23 of WO 2002/085923) is optionally used to synthesize glutamineanalogs with substituents at the nitrogen of the amide. See, e.g., King,F. E. & Kidd, D. A. A. A New Synthesis of Glutamine and of γ-Dipeptidesof Glutamic Acid from Phthylated Intermediates. J. Chem. Soc. 3315-3319(1949); Friedman, O. M. & Chatterji, R. Synthesis of Derivatives ofGlutamine as Model Substrates for Anti-Tumor Agents. J. Am. Chem. Soc.81, 3750-3752 (1959); Craig, J. C. et al. Absolute Configuration of theEnantiomers of 7-Chloro-4[[4-(diethylamino)-1-methylbutyl]amino]quinoline (Chloroquine). J. Org.Chem. 53, 1167-1170 (1988); and Azoulay, M., Vilmont, M. & Frappier, F.Glutamine analogues as Potential Antimalarials, Eur. J. Med. Chem. 26,201-5 (1991). The anhydride is typically prepared from glutamic acid byfirst protection of the amine as the phthalimide followed by refluxingin acetic acid. The anhydride is then opened with a number of amines,resulting in a range of substituents at the amide. Deprotection of thephthaloyl group with hydrazine affords a free amino acid as shown inFIG. 23 of WO 2002/085923.

Substitution at the γ-position is typically accomplished via alkylationof glutamic acid. See, e.g., Koskinen, A. M. P. & Rapoport, H. Synthesisof 4-Substituted Prolines as Conformationally Constrained Amino AcidAnalogues. J. Org. Chem. 54, 1859-1866. (1989). A protected amino acid,e.g., as illustrated by compound number 5 in FIG. 24 of WO 2002/085923is optionally prepared by first alkylation of the amino moiety with9-bromo-9-phenylfluorene (PhflBr) (see, e.g., Christie, B. D. &Rapoport, H. Synthesis of Optically Pure Pipecolates from L-Asparagine.Application to the Total Synthesis of (+)-Apovincamine through AminoAcid Decarbonylation and Iminium Ion Cyclization. J. Org. Chem. 1989,1859-1866 (1985)) and then esterification of the acid moiety usingO-tert-butyl-N,N′-diisopropylisourea. Addition of KN(Si(CH₃)₃)₂regioselectively deprotonates at the α-position of the methyl ester toform the enolate, which is then optionally alkylated with a range ofalkyl iodides. Hydrolysis of the t-butyl ester and Phfl group gave thedesired γ-methyl glutamine analog (Compound number 2 in FIG. 24 of WO2002/085923).

An N-C^(γ) cyclic analog, as illustrated by Compound number 3 in FIG. 25of WO 2002/085923, is optionally prepared in 4 steps from Boc-Asp-Ot-Buas previously described. See, e.g., Barton et al., Synthesis of Novelα-Amino-Acids and Derivatives Using Radical Chemistry: Synthesis of L-and D-α-Amino-Adipic Acids, L-α-aminopimelic Acid and AppropriateUnsaturated Derivatives. Tetrahedron Lett. 43, 42974308 (1987) andSubasinghe et al., Quisqualic acid analogues: synthesis ofbeta-heterocyclic 2-aminopropanoic acid derivatives and their activityat a novel quisqualate-sensitized site. J. Med. Chem. 35 4602-7 (1992).Generation of the anion of the N-t-Boc-pyrrolidinone, pyrrolidinone, oroxazolidone followed by the addition of the compound 7, as shown in FIG.25, results in a Michael addition product. Deprotection with TFA thenresults in the free amino acids.

In addition to the above unnatural amino acids, a library of tyrosineanalogs has also been designed. Based upon the crystal structure of B.stearothermophilus TyrRS, whose active site is highly homologous to thatof the M. jannashii synthetase, residues within a 10 Å shell of thearomatic side chain of tyrosine were mutated (Y32, G34, L65, Q155, D158,A167, Y32 and D158). The library of tyrosine analogs, as shown in FIG.26 of WO 2002/085923, has been designed to complement an array ofsubstitutions to these active site amino acids. These include a varietyof phenyl substitution patterns, which offer different hydrophobic andhydrogen-bonding properties. Tyrosine analogs are optionally preparedusing the general strategy illustrated by WO 2002/085923 (see, e.g.,FIG. 27 of the publication). For example, an enolate of diethylacetamidomalonate is optionally generated using sodium ethoxide. Adesired tyrosine analog can then be prepared by adding an appropriatebenzyl bromide followed by hydrolysis.

Cellular Uptake of Unnatural Amino Acids

Unnatural amino acid uptake is one issue that is typically consideredwhen designing and selecting unnatural amino acids, e.g., forincorporation into a protein. For example, the high charge density ofα-amino acids suggests that these compounds are unlikely to be cellpermeable. Natural amino acids are taken up into bacteria via acollection of protein-based transport systems displaying varying degreesof amino acid specificity. The invention therefore provides a rapidscreen for assessing which unnatural amino acids, if any, are taken upby cells.

For example, a variety of unnatural amino acids are optionally screenedin minimal media for toxicity to cells. Toxicities are typically sortedinto five groups: (1) no toxicity, in which no significant change indoubling times occurs; (2) low toxicity, in which doubling timesincrease by less than about 10%; (3) moderate toxicity, in whichdoubling times increase by about 10% to about 50%; (4) high toxicity, inwhich doubling times increase by about 50% to about 100%; and (5)extreme toxicity, in which doubling times increase by more than about100%. See, e.g., Liu, D. R. & Schultz, P. G. Progress toward theevolution of an organism with an expanded genetic code. PNAS, USA 96,47804785 (1999). The toxicity of the amino acids scoring as highly orextremely toxic is typically measured as a function of theirconcentration to obtain IC₅₀ values. In general, amino acids which arevery close analogs of natural amino acids or which display reactivefunctionality demonstrate the highest toxicities. The former trendsuggests that mechanisms of toxicity for these unnatural amino acids canbe incorporation into proteins or inhibition of essential enzymes thatprocess natural amino acids.

To identify possible uptake pathways for toxic amino acids, toxicityassays are optionally repeated at IC₅₀ levels, e.g., in mediasupplemented with an excess of a structurally similar natural aminoacid. For toxic amino acids, the presence of excess natural amino acidtypically rescues the ability of the cells to grow in the presence ofthe toxin, presumably because the natural amino acid effectivelyoutcompetes the toxin for either cellular uptake or for binding toessential enzymes. In these cases, the toxic amino acid is optionallyassigned a possible uptake pathway and labeled a “lethal allele” whosecomplementation is required for cell survival. These lethal alleles areextremely useful for assaying the ability of cells to uptake nontoxicunnatural amino acids. Complementation of the toxic allele, evidenced bythe restoration of cell growth, suggests that the nontoxic amino acid istaken up by the cell, possibly by the same uptake pathway as thatassigned to the lethal allele. A lack of complementation isinconclusive. For example studies and conclusions see the examplesprovided below.

Results obtained, e.g., as described in the examples below, demonstratethat complementation of lethal unnatural amino acid alleles is anefficient method for qualitatively assessing amino acid uptake. Themethod typically requires far less effort than radiolabeling largenumbers of compounds and is therefore a more advantageous method foranalyzing unnatural; amino acids of interest. This general strategy isoptionally used to rapidly evaluate the cellular uptake of a wide rangeof molecules such as nucleic acid base analogs, carbohydrate analogs, orpeptide analogs. For example, this strategy is optionally used toevaluate the cellular uptake of the unnatural amino aids presentedherein.

The invention also provides a general method for delivering unnaturalamino acids, which is independent of all amino acid uptake pathways.This general method relies on uptake via peptide permeases, whichtransport dipeptides and tripeptides across the cytoplasmic membrane.Peptide permeases are not very side-chain specific, and the KD valuesfor their substrates are comparable to KD values of amino acidpermeases, e.g., about 0.1 mM to about 10 mM). See, e.g., Nckitenko etal., A structure of DppA, a periplasmic depeptide transport/chemosensoryreceptor. Biochemistry 34, 16585-16595 (1995) and Dunten, P., Mowbray,S. L. Crystal structure of the dipeptide binding protein fromEscherichia coli involved in active transport and chemotaxis. ProteinScience 4, 2327-34 (1995). The unnatural amino acids are then taken upas conjugates of natural amino acids, such as lysine, and released intothe cytoplasm upon hydrolysis of the dipeptide by one of endogenous E.coli peptidases. To test this approach, several Unn-Lys and Lys-Unndipeptides are synthesized by solid phase synthesis, and the growth ofan E. coli strain deficient in lysine biosynthesis on lysine minimalmedia in the presence and absence of these dipeptides is tested. Theonly source of lysine available to these cells is the dipeptidecontaining the unnatural amino acid. Uptake of phosphonoserine,phosphonotyrosine, pentafluorophenylalanine, and caged serine have beenanalyzed in this manner. In all four cases, growth was observed on 10 mMand higher dipeptide concentrations. Although uptake is easily analyzedwith the method provided herein, an alternative to designing unnaturalamino acid that are amenable to cellular uptake pathways, is to providebiosynthetic pathways to create amino acids in vivo.

Biosynthesis of Unnatural Amino Acids

Many biosynthetic pathways already exist in cells for the production ofamino acids and other compounds. While a biosynthetic method for aparticular unnatural amino acid may not exist in nature, e.g., in E.coli, the invention provide such methods. For example, biosyntheticpathways for unnatural amino acids are optionally generated in E. coliby adding new enzymes or modifying existing E. coli pathways. Additionalnew enzymes are optionally naturally occurring enzymes or artificiallyevolved enzymes. For example, the biosynthesis of p-aminophenylalanine(as presented, e.g., in WO 2002/085923) relies on the addition of acombination of known enzymes from other organisms. The genes for theseenzymes can be introduced into a cell, e.g., an E. coli cell, bytransforming the cell with a plasmid comprising the genes. The genes,when expressed in the cell, provide an enzymatic pathway to synthesizethe desired compound. Examples of the types of enzymes that areoptionally added are provided in the examples below. Additional enzymessequences are found, e.g., in Genbank. Artificially evolved enzymes arealso optionally added into a cell in the same manner. In this manner,the cellular machinery and resources of a cell are manipulated toproduce unnatural amino acids.

A variety of methods are available for producing novel enzymes for usein biosynthetic pathways or for evolution of existing pathways. Forexample, recursive recombination, e.g., as developed by Maxygen, Inc.(on the world wide web at www.maxygen.com), is optionally used todevelop novel enzymes and pathways. See, e.g., Stemmer 1994, “Rapidevolution of a protein in vitro by DNA shuffling,” Nature Vol. 370 No.4: Pg. 389-391; and Stemmer, 1994, “DNA shuffling by randomfragmentation and reassembly: In vitro recombination for molecularevolution,” Proc. Natl. Acad. Sci. USA. Vol. 91: Pg. 10747-10751.Similarly DesignPath™, developed by Genencor (on the world wide web atgenencor.com) is optionally used for metabolic pathway engineering,e.g., to engineer a pathway to create an unnatural amino acid in E coli.This technology reconstructs existing pathways in host organisms using acombination of new genes, e.g., identified through functional genomics,and molecular evolution and design. Diversa Corporation (on the worldwide web at diversa.com) also provides technology for rapidly screeninglibraries of genes and gene pathways, e.g., to create new pathways.

Typically, the biosynthesis methods of the invention, e.g., the pathwayto create p-aminophenylalanine (pAF) from chorismate, do not affect theconcentration of other amino acids produced in the cell. For example apathway used to produce pAF from chorismate produces pAF in the cellwhile the concentrations of other aromatic amino acids typicallyproduced from chorismate are not substantially affected. Typically theunnatural amino acid produced with an engineered biosynthetic pathway ofthe invention is produced in a concentration sufficient for efficientprotein biosynthesis, e.g., a natural cellular amount, but not to such adegree as to affect the concentration of the other amino acids orexhaust cellular resources. Typical concentrations produced in vivo inthis manner are about 10 mM to about 0.05 mM. Once a bacterium istransformed with a plasmid comprising the genes used to produce enzymesdesired for a specific pathway and a twenty-first amino acid, e.g., pAF,dopa, O-methyl-L-tyrosine, or the like, is generated, in vivo selectionsare optionally used to further optimize the production of the unnaturalamino acid for both ribosomal protein synthesis and cell growth.

Nucleic Acid and Polypeptide Sequence and Variants

As described above and below, the invention provides for nucleic acidpolynucleotide sequences, e.g., O-tRNAs and O-RSs, and polypeptide aminoacid sequences, e.g., O-RSs, and, e.g., compositions and methodscomprising said sequences. Examples of said sequences, e.g., O-tRNAs andO-RSs are disclosed herein (see Table 2, e.g., SEQ ID NO. 1-10).However, one of skill in the art will appreciate that the invention isnot limited to those sequences disclosed herein, e.g., the Examples. Oneof skill will appreciate that the invention also provides many unrelatedsequences with the functions described herein, e.g., encoding an O-tRNAor an O-RS.

The invention provides polypeptides (e.g., O-RSs) and polynucleotides,e.g., O-tRNA, polynucleotides that encode O-RSs or portions thereof,oligonucleotides used to isolate aminoacyl-tRNA synthetase clones, etc.Polypeptides of the invention include polypeptides or proteins withunnatural amino acids of the invention. An polypeptide of the inventionalso includes an artificial polypeptide, e.g., (a) a polypeptide thatcomprises an amino acid sequence as shown in any one of SEQ ID NO.: 4-6;(b) a polypeptide that comprises an amino acid sequence encoded by apolynucleotide sequence as shown in any one of SEQ ID NO.: 8-10; (c) apolypeptide that is specifically immunoreactive with an antibodyspecific for a polypeptide of (a), or (b); and, (d) an amino acidsequence comprising a conservative variation of (a), (b), or (c).Antibodies and antisera that are specifically immunoreactive with anartificial polypeptide of the invention are also provided. In oneembodiment, a composition includes a polypeptide of the invention and anexcipient (e.g., buffer, water, pharmaceutically acceptable excipient,etc.).

Polynucleotides of the invention include those that encode proteins orpolypeptides of interests of the invention with one or more selectorcodon. A polynucleotide of the invention also includes a polynucleotideof any one of SEQ ID NOs.: 8, 9, or 10, or a conservative variationthereof. A polynucleotide of the invention includes a polynucleotidethat encodes an amino acid sequence comprising SEQ ID NO.:1-6. Apolynucleotide of the invention also includes a polynucleotide thatencodes a polypeptide of the invention. Similarly, an artificial nucleicacid that hybridizes to a polynucleotide indicated above under highlystringent conditions over substantially the entire length of the nucleicacid (and is other than a naturally polynucleotide) is a polynucleotideof the invention. An artificial polynucleotide is a polynucleotide thatis man made and is not naturally occurring.

In certain embodiments, a vector (e.g., a plasmid, a cosmid, a phage, avirus, etc.) comprises a polynucleotide of the invention. In oneembodiment, the vector is an expression vector. In another embodiment,the expression vector includes a promoter operably linked to one or moreof the polynucleotides of the invention. In another embodiment, a cellcomprises a vector that includes a polynucleotide of the invention.

One of skill will also appreciate that many variants of the disclosedsequences are included in the invention. For example, conservativevariations of the disclosed sequences that yield a functionallyidentical sequence are included in the invention. Variants of thenucleic acid polynucleotide sequences, wherein the variants hybridize toat least one disclosed sequence, are considered to be included in theinvention. Unique subsequences of the sequences disclosed herein, asdetermined by, e.g., standard sequence comparison techniques, are alsoincluded in the invention.

Conservative Variations

Owing to the degeneracy of the genetic code, “silent substitutions”(i.e., substitutions in a nucleic acid sequence which do not result inan alteration in an encoded polypeptide) are an implied feature of everynucleic acid sequence which encodes an amino acid. Similarly,“conservative amino acid substitutions,” in one or a few amino acids inan amino acid sequence are substituted with different amino acids withhighly similar properties, are also readily identified as being highlysimilar to a disclosed construct. Such conservative variations of eachdisclosed sequence are a feature of the present invention.

“Conservative variations” of a particular nucleic acid sequence refersto those nucleic acids which encode identical or essentially identicalamino acid sequences, or, where the nucleic acid does not encode anamino acid sequence, to essentially identical sequences. One of skillwill recognize that individual substitutions, deletions or additionswhich alter, add or delete a single amino acid or a small percentage ofamino acids (typically less than 5%, more typically less than 4%, 2% or1%) in an encoded sequence are “conservatively modified variations”where the alterations result in the deletion of an amino acid, additionof an amino acid, or substitution of an amino acid with a chemicallysimilar amino acid. Thus, “conservative variations” of a listedpolypeptide sequence of the present invention include substitutions of asmall percentage, typically less than 5%, more typically less than 2% or1%, of the amino acids of the polypeptide sequence, with aconservatively unnatural amino acid that comprises an amino acid, wherea saccharide moiety is linked and/or an unnatural amino acid thatincludes a saccharide moiety of the same conservative substitutiongroup. Finally, the addition of sequences which do not alter the encodedactivity of a nucleic acid molecule, such as the addition of anon-functional sequence, is a conservative variation of the basicnucleic acid.

Conservative substitution tables providing functionally similar aminoacids are well known in the art. The following sets forth example groupswhich contain natural amino acids that include “conservativesubstitutions” for one another.

Conservative Substitution Groups

1 Alanine (A) Serine (S) Threonine (T) 2 Aspartic acid (D) Glutamic acid(E) 3 Asparagine (N) Glutamine (Q) 4 Arginine (R) Lysine (K) 5Isoleucine (I) Leucine (L) Methionine (M) Valine (V) 6 Phenylalanine (F)Tyrosine (Y) Tryptophan (W)

Nucleic Acid Hybridization

Comparative hybridization can be used to identify nucleic acids of theinvention, such as SEQ ID NO.: 7, 8, 9, or 10, including conservativevariations of nucleic acids of the invention, and this comparativehybridization method is a preferred method of distinguishing nucleicacids of the invention. In addition, target nucleic acids whichhybridize to a nucleic acid represented by, e.g., SEQ ID NO: 7, 8, 9, or10, under high, ultra-high and ultra-ultra high stringency conditionsare a feature of the invention. Examples of such nucleic acids includethose with one or a few silent or conservative nucleic acidsubstitutions as compared to a given nucleic acid sequence.

A test nucleic acid is said to specifically hybridize to a probe nucleicacid when it hybridizes at least ½ as well to the probe as to theperfectly matched complementary target, i.e., with a signal to noiseratio at lest ½ as high as hybridization of the probe to the targetunder conditions in which the perfectly matched probe binds to theperfectly matched complementary target with a signal to noise ratio thatis at least about 5×-10× as high as that observed for hybridization toany of the unmatched target nucleic acids.

Nucleic acids “hybridize” when they associate, typically in solution.Nucleic acids hybridize due to a variety of well characterizedphysico-chemical forces, such as hydrogen bonding, solvent exclusion,base stacking and the like. An extensive guide to the hybridization ofnucleic acids is found in Tijssen (1993) Laboratory Techniques inBiochemistry and Molecular Biology—Hybridization with Nucleic AcidProbes part I chapter 2, “Overview of principles of hybridization andthe strategy of nucleic acid probe assays,” (Elsevier, New York), aswell as in Ausubel, supra. Hames and Higgins (1995) Gene Probes 1 IRLPress at Oxford University Press, Oxford, England, (Hames and Higgins 1)and Hames and Higgins (1995) Gene Probes 2 IRL Press at OxfordUniversity Press, Oxford, England (Hames and Higgins 2) provide detailson the synthesis, labeling, detection and quantification of DNA and RNA,including oligonucleotides.

An example of stringent hybridization conditions for hybridization ofcomplementary nucleic acids which have more than 100 complementaryresidues on a filter in a Southern or northern blot is 50% formalin with1 mg of heparin at 42° C., with the hybridization being carried outovernight. An example of stringent wash conditions is a 0.2×SSC wash at65° C. for 15 minutes (see Sambrook, supra for a description of SSCbuffer). Often the high stringency wash is preceded by a low stringencywash to remove background probe signal. An example low stringency washis 2×SSC at 40° C. for 15 minutes. In general, a signal to noise ratioof 5× (or higher) than that observed for an unrelated probe in theparticular hybridization assay indicates detection of a specifichybridization.

“Stringent hybridization wash conditions” in the context of nucleic acidhybridization experiments such as Southern and northern hybridizationsare sequence dependent, and are different under different environmentalparameters. An extensive guide to the hybridization of nucleic acids isfound in Tijssen (1993), supra. and in Hames and Higgins, 1 and 2.Stringent hybridization and wash conditions can easily be determinedempirically for any test nucleic acid. For example, in determiningstringent hybridization and wash conditions, the hybridization and washconditions are gradually increased (e.g., by increasing temperature,decreasing salt concentration, increasing detergent concentration and/orincreasing the concentration of organic solvents such as formalin in thehybridization or wash), until a selected set of criteria are met. Forexample, in highly stringent hybridization and wash conditions, thehybridization and wash conditions are gradually increased until a probebinds to a perfectly matched complementary target with a signal to noiseratio that is at least 5× as high as that observed for hybridization ofthe probe to an unmatched target.

“Very stringent” conditions are selected to be equal to the thermalmelting point (T_(m)) for a particular probe. The T_(m) is thetemperature (under defined ionic strength and pH) at which 50% of thetest sequence hybridizes to a perfectly matched probe. For the purposesof the present invention, generally, “highly stringent” hybridizationand wash conditions are selected to be about 5° C. lower than the T_(m)for the specific sequence at a defined ionic strength and pH.

“Ultra high-stringency” hybridization and wash conditions are those inwhich the stringency of hybridization and wash conditions are increaseduntil the signal to noise ratio for binding of the probe to theperfectly matched complementary target nucleic acid is at least 10× ashigh as that observed for hybridization to any of the unmatched targetnucleic acids. A target nucleic acid which hybridizes to a probe undersuch conditions, with a signal to noise ratio of at least ½ that of theperfectly matched complementary target nucleic acid is said to bind tothe probe under ultra-high stringency conditions.

Similarly, even higher levels of stringency can be determined bygradually increasing the hybridization and/or wash conditions of therelevant hybridization assay. For example, those in which the stringencyof hybridization and wash conditions are increased until the signal tonoise ratio for binding of the probe to the perfectly matchedcomplementary target nucleic acid is at least 10×, 20×, 50×, 100×, or500× or more as high as that observed for hybridization to any of theunmatched target nucleic acids. A target nucleic acid which hybridizesto a probe under such conditions, with a signal to noise ratio of atleast ½ that of the perfectly matched complementary target nucleic acidis said to bind to the probe under ultra-ultra-high stringencyconditions.

Nucleic acids which do not hybridize to each other under stringentconditions are still substantially identical if the polypeptides whichthey encode are substantially identical. This occurs, e.g., when a copyof a nucleic acid is created using the maximum codon degeneracypermitted by the genetic code.

Unique Subsequences

In one aspect, the invention provides a nucleic acid that comprises aunique subsequence in a nucleic acid selected from the sequences ofO-tRNAs and O-RSs disclosed herein. The unique subsequence is unique ascompared to a nucleic acid corresponding to any known O-tRNA or O-RSnucleic acid sequence. Alignment can be performed using, e.g., BLAST setto default parameters. Any unique subsequence is useful, e.g., as aprobe to identify the nucleic acids of the invention.

Similarly, the invention includes a polypeptide which comprises a uniquesubsequence in a polypeptide selected from the sequences of O-RSsdisclosed herein. Here, the unique subsequence is unique as compared toa polypeptide corresponding to any previously known polypeptidesequence.

The invention also provides for target nucleic acids which hybridizesunder stringent conditions to a unique coding oligonucleotide whichencodes a unique subsequence in a polypeptide selected from thesequences of O-RSs wherein the unique subsequence is unique as comparedto a polypeptide corresponding to any of the control polypeptides (e.g.,parental sequences from which synthetases of the invention were derived,e.g., by mutation). Unique sequences are determined as noted above.

Sequence Comparison, Identity and Homology

The terms “identical” or percent “identity,” in the context of two ormore nucleic acid or polypeptide sequences, refer to two or moresequences or subsequences that are the same or have a specifiedpercentage of amino acid residues or nucleotides that are the same, whencompared and aligned for maximum correspondence, as measured using oneof the sequence comparison algorithms described below (or otheralgorithms available to persons of skill) or by visual inspection.

The phrase “substantially identical,” in the context of two nucleicacids or polypeptides (e.g., DNAs encoding an O-tRNA or O-RS, or theamino acid sequence of an O-RS) refers to two or more sequences orsubsequences that have at least about 60%, about 80%, about 90-95%,about 98%, about 99% or more nucleotide or amino acid residue identity,when compared and aligned for maximum correspondence, as measured usinga sequence comparison algorithm or by visual inspection. Such“substantially identical” sequences are typically considered to be“homologous,” without reference to actual ancestry. Preferably, the“substantial identity” exists over a region of the sequences that is atleast about 50 residues in length, more preferably over a region of atleast about 100 residues, and most preferably, the sequences aresubstantially identical over at least about 150 residues, or over thefull length of the two sequences to be compared.

Proteins and/or protein sequences are “homologous” when they arederived, naturally or artificially, from a common ancestral protein orprotein sequence. Similarly, nucleic acids and/or nucleic acid sequencesare homologous when they are derived, naturally or artificially, from acommon ancestral nucleic acid or nucleic acid sequence. For example, anynaturally occurring nucleic acid can be modified by any availablemutagenesis method to include one or more selector codon. Whenexpressed, this mutagenized nucleic acid encodes a polypeptidecomprising one or more unnatural amino acid. The mutation process can,of course, additionally alter one or more standard codon, therebychanging one or more standard amino acid in the resulting mutant proteinas well. Homology is generally inferred from sequence similarity betweentwo or more nucleic acids or proteins (or subsequences thereof). Theprecise percentage of similarity between sequences that is useful inestablishing homology varies with the nucleic acid and protein at issue,but as little as 25% sequence similarity is routinely used to establishhomology. Higher levels of sequence similarity, e.g., 30%, 40%, 50%,60%, 70%, 80%, 90%, 95%, or 99% or more, can also be used to establishhomology. Methods for determining sequence similarity percentages (e.g.,BLASTP and BLASTN using default parameters) are described herein and aregenerally available.

For sequence comparison and homology determination, typically onesequence acts as a reference sequence to which test sequences arecompared. When using a sequence comparison algorithm, test and referencesequences are input into a computer, subsequence coordinates aredesignated, if necessary, and sequence algorithm program parameters aredesignated. The sequence comparison algorithm then calculates thepercent sequence identity for the test sequence(s) relative to thereference sequence, based on the designated program parameters.

Optimal alignment of sequences for comparison can be conducted, e.g., bythe local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482(1981), by the homology alignment algorithm of Needleman & Wunsch, J.Mol. Biol. 48:443 (1970), by the search for similarity method of Pearson& Lipman, Proc. Nat'l. Acad. Sci. USA 85:2444 (1988), by computerizedimplementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA inthe Wisconsin Genetics Software Package, Genetics Computer Group, 575Science Dr., Madison, Wis.), or by visual inspection (see generallyAusubel et al., infra).

One example of an algorithm that is suitable for determining percentsequence identity and sequence similarity is the BLAST algorithm, whichis described in Altschul et al., J. Mol. Biol. 215:403-410 (1990).Software for performing BLAST analyses is publicly available through theNational Center for Biotechnology Information (www.ncbi.nlm.nih.gov/).This algorithm involves first identifying high scoring sequence pairs(HSPs) by identifying short words of length W in the query sequence,which either match or satisfy some positive-valued threshold score Twhen aligned with a word of the same length in a database sequence. T isreferred to as the neighborhood word score threshold (Altschul et al.,supra). These initial neighborhood word hits act as seeds for initiatingsearches to find longer HSPs containing them. The word hits are thenextended in both directions along each sequence for as far as thecumulative alignment score can be increased. Cumulative scores arecalculated using, for nucleotide sequences, the parameters M (rewardscore for a pair of matching residues; always >0) and N (penalty scorefor mismatching residues; always <0). For amino acid sequences, ascoring matrix is used to calculate the cumulative score. Extension ofthe word hits in each direction are halted when: the cumulativealignment score falls off by the quantity X from its maximum achievedvalue; the cumulative score goes to zero or below, due to theaccumulation of one or more negative-scoring residue alignments; or theend of either sequence is reached. The BLAST algorithm parameters W, T,and X determine the sensitivity and speed of the alignment. The BLASTNprogram (for nucleotide sequences) uses as defaults a wordlength (W) of11, an expectation (E) of 10, a cutoff of 100, M=5, N=−4, and acomparison of both strands. For amino acid sequences, the BLASTP programuses as defaults a wordlength (W) of 3, an expectation (E) of 10, andthe BLOSUM62 scoring matrix (see Henikoff & Henikoff (1989) Proc. Natl.Acad. Sci. USA 89:10915).

In addition to calculating percent sequence identity, the BLASTalgorithm also performs a statistical analysis of the similarity betweentwo sequences (see, e.g., Karlin & Altschul, Proc. Nat'l. Acad. Sci. USA90:5873-5787 (1993)). One measure of similarity provided by the BLASTalgorithm is the smallest sum probability (P(N)), which provides anindication of the probability by which a match between two nucleotide oramino acid sequences would occur by chance. For example, a nucleic acidis considered similar to a reference sequence if the smallest sumprobability in a comparison of the test nucleic acid to the referencenucleic acid is less than about 0.1, more preferably less than about0.01, and most preferably less than about 0.001.

Mutagenesis and Other Molecular Biology Techniques

Polynucleotides and polypeptides of the invention and used in theinvention can be manipulated using molecular biological techniques.General texts which describe molecular biological techniques includeBerger and Kimmel, supra; Sambrook, supra, and Ausubel, supra. Thesetexts describe mutagenesis, the use of vectors, promoters and many otherrelevant topics related to, e.g., the generation of genes that includeselector codons for production of glycoproteins of the invention,orthogonal tRNAs, orthogonal synthetases, and pairs thereof.

Various types of mutagenesis are used in the invention, e.g., to mutatetRNA molecules, to produce libraries of tRNAs, to produce libraries ofsynthetases, to insert selector codons that encode an unnatural aminoacid, e.g., an unnatural amino acid comprising a moiety where asaccharide moiety can be attached, or an unnatural amino acid thatincludes a saccharide moiety, in a protein or polypeptide of interest.They include but are not limited to site-directed, random pointmutagenesis, homologous recombination, DNA shuffling or other recursivemutagenesis methods, chimeric construction, mutagenesis using uracilcontaining templates, oligonucleotide-directed mutagenesis,phosphorothioate-modified DNA mutagenesis, mutagenesis using gappedduplex DNA or the like, or any combination thereof. Additional suitablemethods include point mismatch repair, mutagenesis usingrepair-deficient host strains, restriction-selection andrestriction-purification, deletion mutagenesis, mutagenesis by totalgene synthesis, double-strand break repair, and the like. Mutagenesis,e.g., involving chimeric constructs, is also included in the presentinvention. In one embodiment, mutagenesis can be guided by knowninformation of the naturally occurring molecule or altered or mutatednaturally occurring molecule, e.g., sequence, sequence comparisons,physical properties, crystal structure or the like.

Host cells are genetically engineered (e.g., transformed, transduced ortransfected) with the polynucleotides of the invention or constructswhich include a polynucleotide of the invention, e.g., a vector of theinvention, which can be, for example, a cloning vector or an expressionvector. For example, the coding regions for the orthogonal tRNA, theorthogonal tRNA synthetase, and the protein to be derivatized with,e.g., an unnatural amino acid comprising a moiety where a saccharidemoiety can be attached, such as an aldehyde- or keto-derivatized aminoacid, or an unnatural amino acid that includes a saccharide moiety, areoperably linked to gene expression control elements that are functionalin the desired host cell. Typical vectors contain transcription andtranslation terminators, transcription and translation initiationsequences, and promoters useful for regulation of the expression of theparticular target nucleic acid. The vectors optionally comprise genericexpression cassettes containing at least one independent terminatorsequence, sequences permitting replication of the cassette ineukaryotes, or prokaryotes, or both (e.g., shuttle vectors) andselection markers for both prokaryotic and eukaryotic systems. Vectorsare suitable for replication and/or integration in prokaryotes,eukaryotes, or preferably both. See Giliman & Smith, Gene 8:81 (1979);Roberts, et al., Nature, 328:731 (1987); Schneider, B., et al., ProteinExpr. Purif. 6435:10 (1995); Ausubel, Sambrook, Berger (all supra). Thevector can be, for example, in the form of a plasmid, a bacterium, avirus, a naked polynucleotide, or a conjugated polynucleotide. Thevectors are introduced into cells and/or microorganisms by standardmethods including electroporation (From et al., Proc. Natl. Acad. Sci.USA 82, 5824 (1985), infection by viral vectors, high velocity ballisticpenetration by small particles with the nucleic acid either within thematrix of small beads or particles, or on the surface (Klein et al.,Nature 327, 70-73 (1987)), and/or the like.

A catalogue of Bacteria and Bacteriophages useful for cloning isprovided, e.g., by the ATCC, e.g., The ATCC Catalogue of Bacteria andBacteriophage (1996) Gherna et al. (eds) published by the ATCC.Additional basic procedures for sequencing, cloning and other aspects ofmolecular biology and underlying theoretical considerations are alsofound in Sambrook (supra), Ausubel (supra), and in Watson et al. (1992)Recombinant DNA Second Edition Scientific American Books, NY. Inaddition, essentially any nucleic acid (and virtually any labelednucleic acid, whether standard or non-standard) can be custom orstandard ordered from any of a variety of commercial sources, such asthe Midland. Certified Reagent Company (Midland, Tex. mcrc.com), TheGreat American Gene Company (Ramona, Calif. available on the World WideWeb at genco.com), ExpressGen Inc. (Chicago, Ill. available on the WorldWide Web at expressgen.com), Operon Technologies Inc. (Alameda, Calif.)and many others.

The engineered host cells can be cultured in conventional nutrient mediamodified as appropriate for such activities as, for example, screeningsteps, activating promoters or selecting transformants. These cells canoptionally be cultured into transgenic organisms. Other usefulreferences, e.g. for cell isolation and culture (e.g., for subsequentnucleic acid isolation) include Freshney (1994) Culture of Animal Cells,a Manual of Basic Technique, third edition, Wiley-Liss, New York and thereferences cited therein; Payne et al. (1992) Plant Cell and TissueCulture in Liquid Systems John Wiley & Sons, Inc. New York, N.Y.;Gamborg and Phillips (eds) (1995) Plant Cell, Tissue and Organ Culture;Fundamental Methods Springer Lab Manual, Springer-Verlag (BerlinHeidelberg New York) and Atlas and Parks (eds) The Handbook ofMicrobiological Media (1993) CRC Press, Boca Raton, Fla.

Kits

Kits are also a feature of the invention. For example, a kit forproducing a glycoprotein that comprises at least saccharide moiety isprovided, where the kit includes a container containing a polynucleotidesequence encoding an O-tRNA, and/or an O-tRNA, and/or a polynucleotidesequence encoding an O-RS, and/or an O-RS. In one embodiment, the kitfurther includes an unnatural amino acid with a saccharide moiety, or anunnatural amino acid with a moiety to attach a saccharide moiety. Inanother embodiment, the kit further comprises instructional materialsfor producing the glycoprotein.

EXAMPLES

The following examples are offered to illustrate, but not to limit theinvention. It is understood that the examples and embodiments describedherein are for illustrative purposes only and that various modificationsor changes in light thereof will be suggested to persons skilled in theart and are to be included within the spirit and purview of thisapplication and scope of the appended claims.

Example 1 System for Incorporating a Keto Functional Group into Proteins

This example describes a system for preparing p-acetyl-L-phenylalanineand incorporating this unnatural amino acid into a protein.

The genetic codes of most known organisms encode the same common twentyamino acids as building blocks for the biosynthesis of proteins. Only inrare cases are selenocysteine (see, e.g., Bock, A., et al. (1991) Mol.Microbiol. 5:515-520) or pyrrolysine (see, e.g., Srinivasan, G., et al.,(2002) Science 296:1459-1462; and, Hao, B., et al., (2002) Science296:1462-1466) added. The side chains of the common amino acids comprisea surprisingly limited number of functional groups—nitrogen bases,carboxylic acids and amides, alcohols, and a thiol group, the remainderbeing simple alkanes or hydrophobic groups. The ability to augment thegenetically encoded amino acids with new amino acids, for example, aminoacids with metal chelating, fluorescent, redox active, photoactive orspin-labeled side chains, would significantly enhance our ability tomanipulate the structures and functions of proteins and perhaps livingorganisms themselves. Recently, we reported that by adding newcomponents to the translational machinery of Escherichia coli (E. coli),one could site-specifically incorporate with high fidelity a number ofunnatural amino acids (see, e.g., Wang, L., et al. (2001) Science 292:498-500; Wang, L., et al. (2002) J. Am. Chem. Soc. 124:1836-1837; and,Zhang, Z., et al. (2002) Angew. Chem. Int. Ed. Engl. 41:2840-2842) intoproteins in vivo. This Example demonstrates that this approach can beextended to add a keto containing amino acid to the genetic code of anorganism, e.g., E. coli, and that the unique reactivity of the ketogroup can be used to selectively modify proteins in vitro with a widevariety of agents.

The keto group is ubiquitous in organic chemistry, and participates in alarge number of reactions, from addition reactions to aldolcondensations. Moreover, the unique reactivity of the keto group allowsit to be selectively modified with hydrazide and hydroxylaminederivatives in the presence of the other amino acid side chains. See,e.g., Cornish, V. W., et al. (1996) J. Am. Chem. Soc. 118: 8150-8151;Geoghegan, K. F. & Stroh, J. G. (1992) Bioconjug. Chem. 3:138-146; and,Mahal, L. K., et al. (1997) Science 276: 1125-1128. Although present incofactors (see, e.g., Begley, T. P., et al. (1997) in Top. Curr. Chem.,eds. Leeper, F. J. & Vederas, J. C. (Springer-Verlag, New York), Vol.195, pp. 93-142), metabolites (see, e.g., Diaz, E., et al. (2001)Microbiol. Mol. Biol. Rev. 65: 523-569) and as a posttranslationalmodification to proteins (see, e.g., Okeley, N. M. & van der Donk, W. A.(2000) Chem. Biol. 7:R159-R171), this important functional group isabsent from the side chains of the common amino acids. In order togenetically encode this functional group in E. coli in the form ofp-acetyl-L-phenylalanine, a tRNA-synthetase pair was evolved that iscapable of inserting this amino acid site-specifically into proteins inE. coli in response to (and only in response to) an amber nonsensecodon. Importantly this tRNA-synthetase pair is orthogonal to itscounterparts for the common 20 amino acids, i.e., the orthogonalsynthetase (and only this synthetase) aminoacylates the orthogonal tRNA(and only this tRNA) with the unnatural amino acid only, and theresulting acylated tRNA inserts the unnatural amino acid only inresponse to the amber codon.

Materials and Methods

Preparation of p-acetyl-L-phenylalanine: Fmoc-p-acetyl-L-phenylalaninewas purchased from RSP Amino Acid Analogues, Inc. (Worcester, Mass.).This compound (1.0 g, 2.3 mmol) was stirred with 4 mL of piperidine (20%in dimethyl formamide (DMF)) for 2 hours at room temperature. Thesolvent was evaporated to obtain white powder. The solid was thenresuspended in 10 mL of cold water (0.1% trifluoroacetic acid (TFA)),and the supernatant was collected by filtration. Preparativereverse-phase HPLC (Microsorb C18, Rainin Instrument Co., Inc., Woburn,Mass.) was used to separate the desired product from the reactionmixture (5-30% CH₃CN in H₂O with 0.1% TFA over 30 min). The eluant(t_(R)=12 min) was lyophilized to obtain a white solid (0.45 g, 88%). ¹HNMR (400 MHz D₂O): δ 7.85-7.28 (m, 4H), 4.23 (dd, 1H, 5.4 Hz), 3.2 (m,2H), 2.7 (s, 3H). MS electrospray ionization (ESI): [M+1]⁺ calcd forC₁₁H₁₃NO₃ 208.09, found 208.47.

Synthesis of p-acetyl-(+)-phenylalanine (see, e.g., Cleland, G. H.(1969) J. Org. Chem. 34:744-747): N-bromosuccinimide (NBS) wasrecrystallized prior to usage. NBS (18.5 g, 105 mmol) was added to astirred solution of 4-methyl acetophone (13.4 g, 100 mmol) in 400 mL ofcarbon tetrachloride, followed by the addition of2′,2′-azobisiosbutyronitrile (AIBN) (0.43 g, 2.5 mmol). The reactionmixture was then heated to reflux for 4 hours. After completion ofreaction (TLC: 8:1/hexanes:EtOAc), the solution was washed with water(1×100 mL), 1 M aqueous HCl (3×100 mL), 0.5% aqueous NaHCO₃ (3×100 mL)and brine (1×100 mL). The organic layer was collected and dried overanhydrous MgSO₄, and solvent was evaporated to obtain a yellow solidwhich was recrystallized with hexanes to afford the desired1-(4-bromoethyl-phenyl)thanone as a solid (16.8 g, 78%). Dry ethanol (50ml) was added dropwise to pentane-washed sodium pieces (2.3 g, 0.1 mol)under argon atmosphere over 15 minutes and the solution was stirred foranother 15 minutes. Solid diethyl acetamidomalonate (2.7 g, 10 mmol) wasthen added over 30 minutes with stirring, followed by the dropwiseaddition of 1-(4-bromoethylphenyl)thanone (2.1 g, 10 mmol) in dryethanol over 90 minutes. After the mixture was heated to refluxovernight and cooled, diethyl ether (150 mL) and water (100 mL) wereadded to the solution. The organic layer was separated and washedsuccessively with 0.5% NaHCO₃ (3×100 mL) and brine (1×100 mL). Afterdrying over anhydrous MgSO₄, solvent was removed in vacuo to afford abrown gummy solid. Hexanes-dichloromethane (4:1) was added to theresidue, and the insoluble material was filtered out and washedexhaustively with 10:1 dichloromethane-benzene to afford2-acetylamino-2-(4-acetylbenzyl)malonic acid diethyl ester as a yellowsolid (3.3 g, 95% crude yield). This compound was stirred with 4 M HClin dioxane overnight. The mixture was then evaporated to dryness andrecrystallized with water to afford p-acetyl-(+)-phenylalanine (13.2 g,64% overall yield) as a white solid. ¹H NMR (400 MHz, D₂O): δ 7.85-7.28(m, 4H), 4.27 (dd, 1H, 5.4 HZ), 3.30 (m, 2H), 2.68 (s, 3H). ¹³C NMR (400MHz, D₂O): δ 195.8, 174.3, 145.9, 133.1, 128.9, 127.8, 60.2, 38.3, 26.5.MS (ESI): [M+1]+calcd for C₁₁H₁₃NO₃ 208.09, found 208.07.

Mutant synthetase evolution: In the positive selection, plasmid pYC-J17was used to express the mutRNA_(CUA)^(Tyr)gene and the chloramphenicol acetyl transferase (CAT gene with a TAGstop codon at Aspll2. See, e.g., Wang, L., et al. (2001) Science 292:498-500. Supercoiled DNA encoding the tyrosyl-tRNA synthetase (TyrRS)library was transformed into E. coli DH10B competent cells containingpYC-J17. Cells were then plated on minimal media plates containing 1%glycerol and 0.3 mM leucine (GMML) with 17 μg/mL tetracycline, 25 μg/mLkanamycin, 60 μg/mL of chloramphenicol, and 1 mMp-acetyl-L-phenylalanine. After incubation at 37° C. for 40 hours,colonies were pooled, and plasmids were isolated. Plasmids encodingmutant synthetases (pBK plasmids) were separated from pYC-J17 using gelelectrophoresis and transformed into E. coli DH10B competent cellscontaining pLWJ17B3 for negative selection. Plasmid pLWJ17B3 expressesthe mutRNA_(CUA)^(Tyr)under the control of the Ipp promoter and rrnC terminator, and thebarnase gene with three amber codons at Gln2, Asp44, and Gly65 under thecontrol of arabinose promoter. Transformed cells were grown on LB(Luria-Bertani) plates containing 0.2% arabinose, 50 μg/ml kanamycin,and 35 μg/ml chloramphenicol. After 8 hours, cells were removed from theplate, and pBK plasmids were purified for further rounds of selection.In the second and third round of positive selection, the concentrationof chloramphenicol was increased to 80 and 100 μg/mL, respectively.After 3 positive selections alternating with 2 negative selections,eleven mutant TyrRS were identified that afforded an IC₅₀ value of 9μg/ml chloramphenicol in the absence of p-acetyl-L-phenylalanine and 120μg/ml chloramphenicol in the presence of p-acetyl-L-phenylalanine in anin vivo CAT assay. See, e.g., Wang, L. & Schultz, P. G. (2001) Chem.Biol. 8: 883-890. The protein sequences of these mutant TyrRS convergedon 3 independent clones LW1, LW5 and LW6, although the codon usage ofeach mutant TyrRS differs.

Protein expression and purification: Plasmid pLEIZ was used to expressthe Z-domain gene with an amber codon at the 7^(th) position and aCOOH-terminal His6 tag under the control of a bacteriophage T5 promoterand t₀ terminator, and the mutRNA_(CUA)^(Tyr)gene under the control of the lpp promoter and rrnC terminator. Themutant synthetase gene isolated from clone LW1 (LW1RS) was encoded inplasmid pBK-LW1RS under the control of the constitutive E. coli GlnRSpromoter and terminator. E. coli DH10B cells cotransformed with pLEIZand pBK-LW1RS were grown in minimal media containing 1% glycerol and 0.3mM leucine (GMML media) with 25 μg/mL kanamycin, 34 μg/mL ofchloramphenicol, and 1.0 mM p-acetyl-(+)-phenylalanine. When cells reachan OD₆₀₀ Of 0.5, isopropyl-β-D-thiogalactopyranoside (IPTG) (1 mM) wasadded to induce protein expression. After 5 hours, cells were pelletedand the protein was purified by Ni²⁺ affinity chromatography underdenaturing conditions according to the manufacturer's protocol (Qiagen,Valencia, Calif.). Proteins were then desalted with a PD-10 column(Amersham Pharmacia, Piscataway, N.J.) and eluted in water. The yield ofprotein was measured by Bradford assay (BCA kit, Biorad, Hercules,Calif.). Aliquots of protein were used for sodium dodecylsulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and massspectrometry.

In vitro protein modification with fluorescein hydrazide and biotinhydrazide: The purified wild-type (wt) and mutant Z domain proteins wereexchanged into phosphate buffered saline solution (PBS buffer, 100 mMpotassium phosphate, pH 6.5, 0.5 M sodium chloride) by dialysis.Fluorescein hydrazide 1 (Molecular Probe, Eugene, Oreg.) or biotinhydrazide 2 (Molecular Probe, Eugene, Oreg.) was dissolved in DMF, andadded into 0.07 μmol of each protein in silanized eppendorf tubes to afinal concentration of 1 mM. PBS buffer (pH 6.5) was added to bring thefinal volume to 0.5 ml. The reaction mixture was kept at 25° C. for 18hours. Unreacted dye or biotin was removed from the protein using aPD-10 column (Amersham Pharmacia, Piscataway, N.J.), and proteins wereeluted with PBS buffer. To determine the labeling efficiency, the elutedprotein samples were then analyzed by reverse-phase HPLC (ZORBAX SB-C18,4.6 mm×250 mm, flow rate 1.0 mL/min, 10→40% CH₃CN in aqueous 50 mMtriethylamine acetate buffer, pH 7.0 over 70 min, Agilent, Palo Alto,Calif.). The retention time (t_(R)) for mutant Z domain without labelingwas 39.3 min; the t_(R) for fluorescein hydrazide labeled mutant Zdomain was 40.7 min; the t_(R) for biotin hydrazide labeled mutant Zdomain was 40.9 min.

Fluorescence spectrum measurement: All fluorescence emission spectrawere recorded using a FluoroMax-2 spectrofluorometer (Instruments S. A.,Inc., Edison, N.J.) with excitation at 490 nm; both excitation andemission bandpass of 4 nm; a photomultiplier tube voltage of 950 V; andat a scan rate of 1 nm/sec. Ten nmol of each labeled protein were used.The reported spectra represent an average of 3 scans.

Results and Disscussion

A Keto Amino Acid

The keto group provides a unique chemical reactivity not present in thecommon twenty amino acids due to its ability to participate in additionreactions involving either the carbonyl group or the acidic Ca position.This group also provides an alternative to the natural amino acidcysteine for the selective modification of proteins with a large varietyof chemical reagents. The reactive thiol group of cysteine has beenextensively used to attach various biophysical probes to proteins. See,e.g., Creighton, T. E. (1986) Methods Enzymol. 131: 83-106; Altenbach,C., et al., (1990) Science 248:1088-1092; Brinkley, M. (1992) Bioconju.Chem. 3: 2-13; Giuliano, K. A., et al. (1995) Annu. Rev. Biophys.Biomol. Struct. 24:405-434; Mannuzzu, L. M., et al., (1996) Science271:213-216; Griffin, B. A., et al. (1998) Science 281: 269-272; Llopis,J., et al., (2000) Methods Enzymol. 327:546-564; and, Gaietta, G., etal., (2002) Science 296:503-507. Unfortunately, the labeling of singlecysteine residues is often complicated by the presence of more than onereactive residue in a protein, as well as exchange reactions in thepresence of free thiol when a disulfide linkage is used. Therefore, theavailability of a nonproteinogenic amino acid with orthogonal reactivitymakes possible selective modification of protein in cases where a singlecysteine cannot be selectively labeled or where two different labels areneeded. The keto group reacts readily with hydrazides, hydroxylamines,and semicarbazides under mild conditions in aqueous solution, and formshydrazone, oxime, and semicarbazone linkages, respectively, which arestable under physiological conditions. See, e.g., Jencks, W. P. (1959)J. Am. Chem. Soc. 81:475-481; and, Shao, J. & Tam, J. P. (1995) J. Am.Chem. Soc. 117:3893-3899.

Several methods have been developed to selectively incorporate thecarbonyl group into peptides and small proteins. Initially, an aldehydewas introduced at the N-termini of peptides by oxidizing N-terminalserine or threonine with periodate. The aldehyde group was coupled tobiotin and fluorescent reporters (see, e.g., Geoghegan, K. F. & Stroh,J. G. (1992) Bioconjug. Chem. 3:138-146) or protein fragments containinga COOH-terminal hydrazide through a hydrazone linkage (see, e.g.,Gaertner, H. F., et al., (1994) J. Biol. Chem. 269:7224-7230). Thecarbonyl group introduced by this method is restricted to the N-terminusand the protein must be stable to oxidation. Solid phase peptidesynthesis (SPPS) was later employed for the preparation of peptidesegments containing either a hydrazide or hydroxylamine, whichsubsequently react with a branched aldehyde core matrix to form peptidedendrimers (see, e.g., Shao, J. & Tam, J. P. (1995) J. Am. Chem. Soc.117:3893-3899; and, Rose, K. (1994) J. Am. Chem. Soc. 116:30-33), orwith a keto containing peptide segment to form synthetic proteins (see,e.g., Canne, L. E., et al., (1995) J. Am. Chem. Soc. 117:2998-3007).SPPS allows the keto group to be incorporated throughout the protein,but suffers the inherent difficulties associated with the synthesis oflarge peptides or proteins. This size limitation can be overcome in somecases by expressed protein ligation (EPL), in which a synthetic peptideis chemically ligated to the COOH-terminus of recombinant proteins. See,e.g., Muir, T. W., et al. (1998) Proc. Natl. Acad. Sci. USA95:6705-6710. A ketone group containing peptide was prepared by SPPS andligated to the Src homology 3 domain of the Abelson protein tyrosinekinase. See, e.g., Ayers, B., et al., (1999) Biopolymers 51:343-354.

An in vitro biosynthetic method has also been used to incorporate theketo group into proteins. See, e.g., Cornish, V. W., et al. (1996) J.Am. Chem. Soc. 118: 8150-8151. In this method, the unnatural amino acidcontaining the keto group is chemically acylated to an amber suppressortRNA. When the acylated tRNA and the mutant gene are combined in an invitro extract capable of supporting protein biosynthesis, the unnaturalamino acid is selectively incorporated in response to a UAG codon. Thismethod requires the suppressor tRNA to be chemically aminoacylated withthe unnatural amino acid in vitro, and the acylated tRNA is consumed asa stoichiometric reagent during translation and cannot be regenerated,resulting in low protein yields. By evolving an orthogonaltRNA-synthetase pair with specificity for p-acetyl-L-phenylalanine, aketo amino acid can be incorporated into proteins, e.g., in response tothe UAG codon directly in living E. coli cells. There should be no sizelimitation on the target protein as long as it can be expressed in theorganism, e.g., E. coli, and it should be possible to express largeamounts of the mutant protein. Moreover, as long as the labeling reagentis cell permeable and nontoxic, it may be possible to selectivelyintroduce the label in whole cells.

Evolution of Mutant Synthetases with Specificities forp-acetyl-L-phenylalanine

The Methanococcus jannaschii tyrosyl-tRNA synthetase (TyrRS) and amutant tyrosine amber suppressor tRNA (mutRNA_(CUA)^(Tyr))were used as the starting point for the generation of the orthogonaltRNA-synthetase pairs. Previously, this pair was shown to be orthogonalin E. coli. See, e.g., Wang, L. & Schultz, P. G. (2001) Chem. Biol. 8:883-890; and, Wang, L., et al. (2000) J. Am. Chem. Soc. 122:5010-5011.To change the amino acid specificity of the TyrRS so that it chargesp-acetyl-L-phenylalanine and not any of the common 20 amino acids, alibrary of M. jannaschii TyrRS mutants was generated and screened. Thecrystal structure of the homologous Bacillus stearothermophilus TyrRS(see, e.g., Brick, P., et al. (1989) J. Mol. Biol. 208:83-98) was usedto identify those residues that are within 6.5 Å of the para position ofthe aryl ring of bound tyrosine. Five corresponding residues (Tyr32,Glu107, Asp158, Ile159 and Leu162) in the active site of M. jannaschiiTyrRS were randomly mutated by polymerase chain reaction (PCR) togenerate a library 1.6×10⁹ in size (see, e.g., Wang, L., et al. (2001)Science 292: 498-500). This TyrRS mutant library was first passedthrough a positive selection in the presence of 1 mMp-acetyl-L-phenylalanine which is based on the suppression of an amberstop codon at nonessential residue (Asp112) in chloramphenicol acetyltransferase (CAT) gene encoded on plasmid pYC-J17 (see, e.g., Wang, L.,et al. (2001) Science 292: 498-500) in E. coli. Cells surviving inchloramphenicol must encode a mutant synthetase that aminoacylates themutRNA_(CUA)^(Tyr)with either a common amino acid(s) orp-acetyl-L-phenylalanine. DNAencoding the mutant synthetases was then isolated and transformed into anegative selection strain expressing the gene of a toxic protein,barnase, containing three amber codons at permissive sites (encoded onplasmid pLWJ17B3). Cells encoding a mutant synthetase that charges themutRNA_(CUA)^(Tyr)with natural amino acids will produce barnase and die. Because nop-acetyl-L-phenylalanine was added to the growth medium in the negativeselection, survivors must encode a synthetase with specificity for theunnatural amino acid. After 3 rounds of positive selection at increasingconcentrations of chloramphenicol, alternating with 2 rounds of negativeselection, a number of clones emerged whose survival in chloramphenicolwas dependent on the addition of p-acetyl-L-phenylalanine. These TyrRS'swere characterized using an in vivo assay based on the suppression ofthe Asp112TAG codon in the CAT gene. See, e.g., Wang, L. & Schultz, P.G. (2001) Chem. Biol. 8: 883-890. Eleven TyrRS mutants were identified.Cells expressing the selected synthetase and the mutRNA_(CUA)^(Tyr)

survived in the absence of p-acetyl-L-phenylalanine on 9 μg/mlchloramphenicol on minimal media plates containing 1% glycerol and 0.3mM leucine (GM plate); in the presence of this unnatural amino acid,cells survived in 120 μg/ml chloramphenicol on GMML plates. This resultsuggests that the selected mutant synthetase has higher activity forp-acetyl-L-phenylalanine than for natural amino acids. Sequencing theDNA of these mutants revealed that they converge on 3 independentmutants on the protein level (LW1, LW5, and LW6), although they havedifferent codon usage for amino acids. The active site mutations of themutant synthetases are listed in Table 1. Based on the crystal structureof the homologous TyrRS from B. stearothernophilus, the conserved sidechain of M. jannaschii Tyr32 and Asp158 likely form hydrogen bonds withthe hydroxyl group of the substrate tyrosine. In the mutant synthetases,Tyr32 is mutated to either Leu or Ala, and Asp158 is mutated to Gly158.These mutations should disfavor the binding of tyrosine and may at thesame time create extra room to accommodate the methyl group ofp-acetyl-L-phenylalanine. Determination of the X-ray crystal structureof the mutants should clarify the exact roles of these mutants. TABLE 1Amino acid residues in the WT M. jannaschii (MJ) TyrRS and the evolvedmutant synthetases with specificities for p-Acetyl-L-phenylalanine Aminoacid residue 32 158 159 162 167 WT Mj TyrRS Tyr Asp Ile Leu Ala LW1 LeuGly Cys Arg Ala LW5 Leu Gly Thr Arg Ala LW8 Ala Gly Gly Leu Ile

Characterization of Mutant Protein Containing p-acetyl-L-phenylalanine

To test the ability of the evolved synthetase and the mutRNA_(CUA)^(Tyr)to selectively incorporate p-acetyl-L-phenylalanine into proteins, anamber stop codon was substituted at a permissive site (Lys7) in the genefor the Z domain of staphylococcal protein A (see, e.g., Nilsson, B., etal. (1987) Protein Eng. 1:107-113) with a COOH-terminal His6 tag. Zdomain has a molecular weight of about 7.9 kD, so its mass can bemeasured with very high accuracy using ion cyclotron resonance (ICR)mass spectrometry. Cells transformed with the mutRNA_(CUA)^(Tyr),LW1RS and Z domain gene (Lys7TAG) were grown in the presence of 1 mMp-acetyl-(O)-phenylalanine. The addition of the unnatural amino acid didnot affect the growth rate of cells. The mutant protein was purified byNi²⁺ affinity chromatography with an overall isolated yield of 3.6 mg/Lin minimal media. For comparison, the yield of Z domain was 9.2 mg/L inminimal media when the mutant TyrRS was replaced with the wild-type (wt)TyrRS. No Z domain was obtained in the absence of eitherp-acetyl-(O)-phenylalanine, the mutRNA_(CUA)^(Tyr)or LW1RS, indicating a very high fidelity in the incorporation of theunnatural amino acid at this site. We have also been successful inincorporating p-acetyl-L-phenylalanine into other proteins such asCdc42.

Both the wt Z domain protein expressed by mutRNA_(CUA)^(Tyr)/WT  TyrRSand the mutant Z domain protein expressed by themutRNA_(CUA)^(Tyr)/LW1RSwere analyzed by electrospray ionization Fourier transform ion cyclotronresonance mass spectrometry (FT-ICR MS). For the wt Z domain protein,three peaks were observed with masses corresponding to the intactprotein, the protein without the first methionine, and the acetylatedform of the protein without the first methionine (confirmed by tandemmass spectrometric analysis of the N-terminal tryptic digested peptidefragment). For the mutant Z domain protein, the experimentalmonoisotopic mass of the intact protein was 7949.893 Da, which is within2.2 ppm of the theoretical mass of 7949.874 Da. Two other peakscorrespond to the protein without the first methionine(M_(Experimental)=7818.838 Da, M_(Theoretical)=7818.833 Da) and itsacetylated form (M_(Experimental)=7860.843 Da, M_(Theoretical)=7860.844Da), respectively. No peaks corresponding to mutant proteins with anyother amino acid at the amber codon position were observed in thespectra. The signal-to-noise ratio of more than 1500 observed in theintact protein mass spectrum translates to a fidelity for theincorporation of p-acetyl-L-phenylalanine of better than 99.8%. Liquidchromatography tandem mass spectrometry of the tryptic digest wascarried out to confirm the sequence of the NH₂-terminal peptide. Theprecursor ion at 606.23 Da, which corresponds to the doubly chargedmolecular ion of the NH₂-terminal tryptic peptide MTSVDNY*INK, wasisolated and fragmented with an ion trap mass spectrometer (ITMS). Thefragment ion masses could be unambiguously assigned, confirming thesite-specific incorporation of p-acetyl-L-phenylalanine. These resultsclearly demonstrate that the evolved synthetase together with themutRNA_(CUA)^(Tyr)incorporate p-acetyl-L-phenylalanine and not any natural amino acid intothe position encoded by the amber codon and at no other positions.

Site-Specific Protein Modification with Fluorescein Hydrazide

We next determined whether the keto group of p-acetyl-L-phenylalaninecould serve as a chemical handle for the site-specific modification ofproteins in vitro. The purified mutant p-acetyl-L-phenylalanine Z domainprotein (mutant Z domain) and wt Z domain protein were treated with 1 mMfluorescein hydrazide (Scheme 1) at 25° C. for 18 hours in phosphatebuffer. After the reaction, proteins were separated from excessfluorescein hydrazide by size exclusion chromatography, and analyzedwith sodium dodecyl sulfate-polyacrylamide gel electrophoresis(SDS-PAGE). The gel was first imaged with a fluoroimaging system, andthen silver stained. The band for mutant Z domain shows a fluorescentsignal while no fluorescence can be detected from the wt Z domain band.Aliquots of these two proteins were used to measure the fluorescencespectrum with 490 nm excitation. Only the Z domain protein containingp-acetyl-L-phenylalanine shows a fluorescence spectrum similar to thatof fluorescein. No fluorescence signal was detected for wt Z domain,indicating that the labeling reaction occurred only between thehydrazide and the ketone, and not any existing functional groups in thewt protein. The labeled product was analyzed with quadrupoletime-of-flight mass spectrometry (QTOF MS). An experimental monoisotopicmass of 8425.160 Da (M_(Theoretical)=8424.958 Da) was obtained,confirming that the fluorescein hydrazide reacted with the mutant Zdomain protein in a molar ratio of 1:1. To determine the labelingextent, the reaction mixture was separated by high performance liquidchromatography (HPLC). The ratio of the peak area of the labeled Zdomain over that of the unlabeled Z domain was 90±5%.

Site-Specific Protein Modification with Biotin Hydrazide

To demonstrate the generality of this approach, we also labeled Z domainwith the biotin hydrazide derivative (Structure C). The purified mutantand wt Z domain were treated with 1 mM biotin hydrazide in phosphatebuffer at 25° C. for 18 hours. After dialysis against phosphate bufferto remove excess biotin hydrazide, the proteins were subject toSDS-PAGE. Separated proteins were transferred to nitrocellulose membraneand probed with a biotin-specific avidin-HRP conjugate. As expected,only the mutant Z domain containing p-acetyl-L-phenylalanine wasdetected, indicating it was labeled with biotin hydrazide. No signal wasobserved for wt Z domain. The labeling efficiency was 80±10% asdetermined by HPLC analysis as described in the fluorescein labelingexperiment. The labeled protein was confirmed by QTOF MS(M_(Experimental)=8416.236, M_(Theoretical)=8416.146 Da) to be theproduct formed between one molecule of biotin hydrazide and one moleculeof mutant Z domain. These experiments demonstrate the excellentspecificity of the ketone handle for the in vitro modification ofproteins.

In summary, we have site-specifically incorporated a novel chemicalfunctional group, the keto group, into proteins in vivo. This functionalgroup can be selectively and efficiently labeled with, e.g., fluoresceinand biotin in vitro by a specific chemical reaction between the ketogroup and hydrazide derivatives. This approach makes it possible toselectively label proteins with a wide variety of other hydrazide orhydroxylamine derivatives (including sugars, spin labels, metalchelators, crosslinking agents, polyethers, fatty acids and toxins),either as probes of protein structure and function, to generate proteinswith enhanced catalytic or therapeutic properties, or for thedevelopment of bioassays using proteins. The ability tosite-specifically incorporate a unique chemical handle into proteinsdirectly in a living cell makes possible the in vivo modification ofproteins with small molecule fluorophores for the in vivo imaging ofprotein localization, protein movement and conformational changes inproteins at molecular resolution. The in vivo labeling of proteinscontaining p-acetyl-L-phenylalanine with fluorophores in E. coli is alsomade possible by this technique.

See also corresponding application entitled “SITE SPECIFIC INCORPORATIONOF KETO AMINO ACIDS INTO PROTEINS” attorney docket number 54A-000170PCT,filed Oct. 15, 2003, which is incorporated herein by reference.

Example 2 In Vivo Incorporation of Meta-Tyrosine Analogues

An orthogonal TyrRS was generated for aminoacylation of themtRNA_(CUA)^(Tyr)(described in Example 1 of WO 2002/085923) with meta-tyrosine analogues.

Preparation of mutant TyrRS library plasmids: A library of plasmidsencoding mutant M. jannaschii TryRSs directed at meta-substitutedtyrosine derivatives was constructed, generally following the methodsdescribed in Example 1 of WO 2002/085923. Briefly, six residues (Tyr32,Ala⁶⁷, His⁷⁰, Gln¹⁵⁵, Asp¹⁵⁸, Ala¹⁶⁷) in the active site of M.jannaschii TyrRS that are within 6.9 Å of the meta-position of the arylring of bound tyrosine in the crystal structure of Bacillusstearothermophilus TyrRS were mutated to all 20 amino acids at DNA levelusing the NNK codon scheme as described in Example 1 above. Theconstructed plasmid library pBK-lib contained around 1×10⁹ independentclones.

Evolution of orthogonal tRNA-synthetase pairs for incorporation ofm-acetyl phenylalanine: After 3 rounds of positive selection and 2rounds of negative selection, five candidate clones (SEQ ID NO: 17-21 ofWO 2002/085923 and SEQ ID NO: 49-53 of WO 2002/085923) emerged whosesurvival in chloramphenicol was dependent on the addition of theunnatural amino acid. In the absence of m-acetyl phenylalanine, the IC₅₀Of chloramphenicol resistance for cells harboring the one of the threemutant TyrRS plasmids is 20 μg/ml. In the presence of m-acetylphenylalanine, the IC₅₀ of resistance to chloramphenicol for the samecells is 100 μg/ml. The large difference between these two numbersreflects the ability of the selected synthetases to specify theincorporation of m-acetyl phenylalanine over the natural amino acids inthe cell. The data for m-methoxy phenylalanine were similar; five cloneswere isolated (SEQ D NO:22-26 of WO 2002/085923 and SEQ ID NO: 54-58 ofWO 2002/085923).

Protein expression of unnatural amino acid incorporated DHFR: Them-methoxy phenylalanine and m-acetyl phenylalanine synthetases selectedabove were used to incorporate the relevant unnatural amino acids inresponse to an amber codon in DHFR as previously described in Example 1of WO 2002/085923. As a negative control, cells containing both theorthogonal pair of tRNA-synthetase and amber-mutant vector encoding DHFRwere grown in the absence of unnatural amino acids. The results ofprotein expression are shown in FIG. 10 of WO 2002/085923. These resultsclearly demonstrated the specificity of the orthogonal pair oftRNA-synthetase to incorporate unnatural m-methoxy phenylalanine andm-acetyl phenylalanine. The yields of expressed DHFR protein areapproximately 0.5 mg/L of culture in both cases.

In one embodiment, compounds (e.g., hydrazide derivatives) can be usedto in vivo label proteins with at least one unnatural amino acid, e.g.,meta-tyrosine analogue.

Example 3 Synthesis of Glycoprotein Mimetics

The availability of a nonproteinogenic functional group with a uniquereactivity greatly facilitates the selective chemical modification ofproteins. The keto group is such a chemical handle—it is absent from theside chains of natural amino acids, and it reacts readily andselectively with hydrazide and hydroxylamine derivatives under mildconditions in the presence of the common amino acids. See, e.g.,Cornish, V. W, et al., (1996) J. Am. Chem. Soc. 118:8150-8151 andreferences therein. The keto group has been included in peptides bysolid phase peptide synthesis, and coupled with nucleophilic saccharidederivatives to construct neoglycopeptides. See, e.g., Rodriguez, E. C.,et al., (1998) J. Org. Chem. 63:7134-7135. We recently developed ageneral method that allows for the site-specific incorporation ofunnatural amino acids into proteins directly in living cells (See, e.g.,WO 2002/085923; and, corresponding application entitled “SITE SPECIFICINCORPORATION OF KETO AMINO ACIDS INTO PROTEINS” attorney docket number54-000170PCT, filed Oct. 15, 2003, which are incorporated herein byreference). See also, e.g., Wang, L., et al., (2001) Science292:498-500. A keto containing amino acid, p-acetyl-L-phenylalanine, hasbeen successfully incorporated in response to the amber nonsense codonwith translation fidelity greater than 99.8%. See, e.g., Wang, L., etal., (2003) Proc. Natl. Acad. Sci. U.S.A. 100:56-61. This Exampledescribes the preparation of homogeneous glycoprotein mimetics using thegenetically encoded keto functionality together with aminooxy saccharidederivatives.

Two routes were explored to generate the glycoprotein mimetics (See FIG.1). In the first approach, one saccharide derivatized with an aminooxygroup is first coupled to the keto group, and additional saccharides areattached enzymatically with glycosyltransferases. In a more convergentsecond route, a glycan with defined structure is prepared as an aminooxyderivative, and is coupled directly to the protein in one step. The Zdomain of staphylococcal protein A was used as the model protein, (see,e.g., Nilsson, B., et al., (1987). Protein Eng. 1: 107-113) because itsrelatively small size (molecular weight 7.9 kD) facilitates massspectrometric characterization with very high accuracy.

The seventh codon of the corresponding gene was mutated to amber stopcodon TAG and a His6 tag was added to the C-terminus to facilitateprotein purification. P-Acetyl-L-phenylalanine was incorporated at theamber position to afford the mutant Z domain protein by previouslyreported protocols. See, e.g., Wang, L., et al., (2003) Proc. Natl.Acad. Sci. U.S.A. 100:56-61. Approximately 3.6 mg/L protein was obtainedafter nickel affinity chromatography. The beta-linked aminooxy analogueof N-acetylglucosamine (GlcNAc) 1 of FIG. 1 was then synthesizedfollowing published procedures. See, e.g., Cao, S., et al., (1995)Tetrahedron 51:6679-6686. The mutant Z domain protein (10 mg/mL) andaminooxy saccharide 1 (21 mM) were mixed in aqueous 100 mM sodiumacetate buffer (pH 5.5) and incubated at 37° C. for 7 to 26 hrs. Thereaction mixture was analyzed by reverse phase high-performance liquidchromatography (HPLC) by monitoring absorbance at 280 nm (See FIG. 2).Only two major peaks were observed, and the corresponding eluents werecharacterized by matrix-assisted laser desorption/ionization—Fouriertransform ion cyclotron resonance mass spectrometry (MALDI-FTICR MS)(See FIG. 3). The monoisotopic masses obtained indicate that one peak(t_(R)=44.8 min) corresponds to the unreacted mutant Z domain(M_(theoretical)=7818.833 Da, M_(experimental)=7818.836 Da), and theother peak (t_(R)=43.2 min) corresponds to the mutant Z domainderivatized with the aminooxy saccharide 1 (M_(theoretical)=8036.924 Da,M_(experimental)=8036.914 Da). When expressed in E. coli, Z domainprotein has three forms: the intact protein, protein without the firstmethionine, and the acetylated form of the protein without methionine.The intact protein can be separated from the other two forms usingreverse phase HPLC. To simplify mass spectrometric analysis, purifiedfraction containing Z domain without first methionine and its acetylatedform were used in this example. Two molecular peaks can be observedwhich correspond to these two forms in all mass spectra, as labeled inspectra for III and IV in FIG. 2. See FIG. 1 for structure. As acontrol, when tyrosine is incorporated at the seventh position of Zdomain, no saccharide derivatized protein is observed. This fact,together with the high-accuracy mass (error <1.2 ppm) observed for thesaccharide modified Z domain, confirmed that the aminooxy saccharide 1is attached to the keto group, selectively. The coupling efficiencyincreases with time (determined from the areas of the HPLC peakscorresponding to starting material and product): the conversion ofstarting material to product was 42% after 7 hrs and greater than 95%after 26 hrs. (See FIG. 2).

We next determined whether a second saccharide could be coupled to thefirst enzymatically. The purified adduct II (5 mg/mL) (see FIG. 1 forstructure) was incubated with UDP-galactose (UDP-Gal) (16 mM) andβ-1,4-galactosyltransferase (0.4 units/mL) in 150 mM HEPES(N-2-hydroxyethylpiperazine-N-2-ethanesulfonic acid) buffer (pH 7.4) for48 hours at ambient temperature. Beta-1,4-galactosyltransferase is knownto transfer galactose from the sugar nucleotide to the 4 position of aGlcNAc moiety to form Galβ1,4GlcNAc. See, e.g., Schanbacher, F. L., andEbner, K. E. (1970) J. Biol. Chem. 245: 5057-5061. After separation byHPLC, a new peak was identified (t_(R)=42.5 min). The monoisotopic mass(M_(theoretical)=8198.977, M_(experimental)=8198.969) of the eluentmeasured by MALDI-FTICR MS confirmed that the galactose was coupled toGlcNAc to yield adduct III (See FIG. 3). See FIG. 1 for structure. Thecoupling efficiency determined by HPLC analysis was about 60%, a valueclose to that reported previously for β-1,4-galactosyltransferase. See,e.g., Witte, K., et al., (1997) J. Am. Chem. Soc. 119:2114-2118. Thisresult indicates that the non-native linkage between the firstsaccharide and the protein does not significantly affect theglycosyltransferase reaction. Further reaction of this disaccharidelabeled protein with CMP-sialic acid and α-2,3-sialyltransferase (see,e.g., Kitagawa, H., and Paulson, J. C. (1994) J. Biol. Chem.269:1394-1401) resulted in the addition of sialic acid to galactose toafford IV (t_(R)=41.7 min), as confirmed by MALDI-FTICR MS(M_(theoretical)=8490.072, M_(experimental)=8490.014) (See FIG. 3). Thecoupling efficiency for conversion of III to IV was 65% based on HPLCanalysis. See FIG. 1 for structures.

Glycoprotein mimetics III and IV were also prepared using a convergentroute. See FIG. 1. Aminooxy GlcNAc (0.05 M) was converted to 2 usingβ-1,4-galactosyltransferase (0.75 units/mL) and the glycosyl donorUDP-galactose in 70% overall yield in 150 mM HEPES buffer (pH 7.4).After purification by aminopropyl silica gel HPLC, sialic acid was addedto 2 (0.03 M) to afford 3 in the same buffer mentioned above inapproximately 80% yield using α-2,3-sialyltransferase (0.22 units/mL)and CMP-sialic acid (0.03 M). Purified aminooxy analogue 2 and 3 (13 and7.2 mM, respectively) were coupled to the Z domain protein (5 mg/mL)containing p-acetyl-L-phenylalanine in 100 mM aqueous sodium acetatebuffer (pH 5.5) at ambient temperature to afford glycoprotein mimeticsIII and IV, respectively. See FIG. 1. The resultant III and IV wereidentical to the corresponding adducts prepared by the first sequentialroute, as confirmed by HPLC and MALDI-FTICR MS analysis. The couplingefficiency of 2 to I and 3 to I under the same reaction conditions for26 hours were about 76% and 60%, respectively. The yields were lowerthan that for the coupling of 1 to I (95%) likely due to the increasingsteric effect as the glycan becomes more complicated.

In summary, we have demonstrated a general method for the synthesis ofhomogeneous glycoprotein mimetics containing well-defined saccharidesubstituents.

Experimental Materials and Methods:

General: UDP-Gal, CMP-NeuAc, β-1,4-galactosyltransferase (β-1,4-GalT)and α-2,3-sialyltransferase (α-2,3-SialT) were purchased fromCalbiochem. Unless otherwise stated, all chemicals were obtained fromAldrich, Acros or Sigma and used without further purification. Reactionswere monitored by thin-layer chromatography (TLC) utilizing ninhydrin orcerium molybdate stain as the developing reagent. All non-aqueousreactions were carried out in oven-dried glassware under an inert Aratmosphere. All non-aqueous solvents were distilled before use. NMRspectra were recorded on Bruker AMX-400, AMX-500 or AMX-600 MHzspectrometers and were referenced to residual solvent peaks (CDCl₃: ¹H ε7.24, ¹³C δ 77.0; CD₃OD: ¹H δ 3.30, ¹³C δ 49.0; D₂O: ¹H δ 4.76).

Compound 2 of FIG. 1: Compound 1 of FIG. 1 (5 mg, 0.021 mmol) andUDP-Gal (21 mg, 0.032 mmol) were dissolved in 350 μL HEPES buffer (150mM, pH 7.4) containing a freshly prepared MnCl₂ solution (2 mmol).β-1,4-GalT (0.3 U, 0.1 U μL⁻¹) and alkaline phosphatase (0.5 U, 1 UμL⁻¹) were added and the reaction mixture was shaken gently at ambienttemperature for 2 days. The reaction mixture was centrifuged and thesupernatant was purified by aminopropyl silica gel HPLC employing agradient elution of 100:0 A:B to 50:50 A:B over 90 min at a flow rate of1 mL min⁻¹ where A=MeCN and B=H₂O. The retention time of the desiredproduct was 53 min. Lyophilization of the column fractions afforded purecompound 2 of FIG. 1 (6 mg, 70%) as a white powder; ¹H NMR D₂O, 600 MHz)δ 4.58 (d, J=6.12, 1H), 4.42 (d, J=7.44, 1H), 3.96 (d, J=11.88 1H), 3.87(m, 1H), 3.78 (dd, J=4.83, 12.3, 1H), 3.72-3.69 (m, 6H), 3.62 (dd,J=3.06, 10.08, 1H), 3.56 (m, 1H), 3.50 (m, 1H), 1.98 (s, 3H). ¹³C NMR(D₂O, 150 MHz) δ 175.18, 103.98, 103.31, 78.63, 75.78, 75.13, 72.92,72.82, 71.39, 68.99, 61.46, 60.43, 53.80, 22.55. HR-FTMS (pos) calcd forC₁₄H₂₆N₂O₁₁ [M+Na]⁺=421.1429, found 421.1448.

Compound 3 of FIG. 1: Compound 2 of FIG. 1 (5.3 mg, 0.013 mmol) andCMP-NeuAc (10 mg, 0.016 mmol) were dissolved in 450 μL HEPES buffer (150mM, pH 7.4) containing a freshly prepared MnCl₂ solution (5 mmol).α-2,3-SialT (22 mU, 3.7 mU μL⁻¹) and alkaline phosphatase (50 mU, 50 mUμL⁻¹) were added and the reaction mixture was shaken gently at ambienttemperature for 2 days. The reaction mixture was centrifuged and thesupernatant was purified by aminopropyl silica gel HPLC employing agradient elution of 100:0 A:B to 0:100 A:B over 30 min at a flow rate of1 mL min⁻¹ where A=MeCN and B=H₂O. The corresponding fractions (27 min)were collected and lyophilized to give a white powder (7 mg, 76%). ¹HNMR (D20, 600 MHz) δ 4.55 (d, J=8.34, 1H), 4.48 (d, J=7.86, 1H), 4.04(dd, J=3.06, 9.60, 1H), 3.58-3.96 (m, 17H), 3.51 (m, 1H), 2.67 (dd,J=4.80, 12.72, 1H), 1.98 (s, 3H), 1.96 (s, 3H), 1.75 (t, J=12.30, 1H).ES-MS (neg) calcd for C₂₅H₄₃N₃O₁₉ [M−H]⁻=688, found 688.

General procedure for coupling aminooxy saccharide derivative to mutantZ domain protein: In a typical reaction, aminooxy saccharide derivative(500 μg) and ˜1 mg mutant Z domain protein were dissolved in 100 mMNaOAc buffer, pH 5.5. Water was added to a total volume of 100 μL andthe reaction mixture was shaken at 37° C. for 26 h. Then the mixture wascentrifuged and the supernatant was purified by reverse phase HPLC on aAgilent ZORBAX SB-C18 4.6 mm×250 mm column employing a gradient elutionof 90:10 A:B to 60:40 A:B over 70 min at a flow rate of 1 mL min⁻¹ whereA=H₂O with 0.1% TFA and B=MeCN with 0.1% TFA. The column fractions wereneutralized with TrisCl buffer (pH 7.0) and desalted with a sizeexclusion column. After eluted with water, the eluent was lyophilized toafford pure H, III, and IV of FIG. 1 as a white powder in 96%, 76% and60% yield, respectively.

Preparation of glycoprotein mimetics III and IV (of FIG. 1) using thesequential route: For preparation of III of FIG. 1, II of FIG. 1 (˜0.5mg) and UDP-Gal (1 mg) were dissolved in 90 uL of 150 mM HEPES buffer,pH 7.4 containing a freshly prepared MnCl₂ solution (0.5 mmol).β-1,4-GalT (40 mU, 40 mU μL⁻¹) and alkaline phosphatase (50 mU, 50 mUμL⁻¹) were added and the reaction mixture was shaken gently at ambienttemperature for 2 days. The reaction mixture was centrifuged and thesupernatant was purified by by reverse phase HPLC. For preparation of IVof FIG. 1, III of FIG. 1 (˜0.5 mg) and CMP-NeuAc (0.5 mg) were dissolvedin 90 uL of 150 mM HEPES buffer pH 7.4 containing a freshly preparedMnCl₂ solution (0.5 mmol). α-2,3-SialT (10 mU, 3.7 mU μL⁻¹) and alkalinephosphatase (50 mU, 50 mU μL⁻¹) were added and the reaction mixture wasshaken gently at ambient temperature for 2 days. The reaction mixturewas centrifuged and the supernatant was purified by reverse phase HPLC.

MALDI-FTICR MS: A home-build instrument with an APEX II console and 9.4T magnet from Bruker Daltonics (Billerica, Mass.) was used forMALDI-FTICR MS experiments. Sugar moieties tend to fall apart whennormal MA/DI sample preparation involving TFA was used. We used a lesssensitive but colder matrix. The matrix is a mixture of3-hydroxypicolinic acid (20 mg mL⁻¹) and diammonium citrate (1 mg mL⁻¹).Decomposition of the glycoprotein was further minimized by thespecialized intermediate pressure MALDI source of the FTICR that reducesmetastable fragmentation by providing collisional cooling in the source.

Example 4 Another Strategy for the Synthesis of Glycoproteins

In one embodiment of the invention, another strategy has been developedto synthesize homogeneous glycoproteins in an organism, e.g., E. coli,by the cotranslational incorporation of a glycosylated amino acid. Forexample, myoglobin containing β-GlcNAc-serine at a defined position canbe expressed in E. coli in good yield and with high fidelity. Theβ-GlcNAc moiety can be recognized by a carbohydrate binding protein orsubsequently modified with a galactosyltransferase. This approach can beapplicable to other posttranslational modifications, e.g., proteinphosphorylation, acetylation, methylation and the like.

Glycosylation is one of the most common post-translational modificationsof proteins in eukaryotes and affects a wide range of protein functionsfrom folding and secretion to biomolecular recognization and serum halflife. See, e.g., R. A. Dwek, (1996) Chem. Rev. 96:683. While there havebeen significant advances in our understanding of the effects ofglycosylation, the specific roles of oligosaccharide chains and therelationships between their structures and functions are just beginningto be understood. See, e.g, C. R. Bertozzi, & L. L. Kiessling, (2001)Science 291:2357. The primary challenge is that glycoproteins aretypically produced as a mixture of glycoforms, making it difficult toisolate unique glycoforms from natural sources. A variety of methodshave been developed to synthesize structurally defined glycoforms, butall impose severe restrictions on the size, quantity, and/or quality ofthe glycoprotein produced. See, e.g., P. Sears, & C. H. Wong, (2001)Science 291:2344; M. Wacker et al., (2002) Science 298:1790; B. G.Davis, (2002) Chem. Rev. 102:579; and, H. C. Hang, & C. R. Bertozzi,(2001) Acc. Chem. Res. 34:727. In this example, a strategy and thecomponents used to produce unique glycoforms in E. coli are described,which includes developing an orthogonal synthetase-tRNA pair thatgenetically encodes a glycosylated amino acid in response to a selectorcodon, e.g., an amber codon, TAG. The genetic incorporation of this andother saccharide-modified amino acids directly into proteins cansignificantly enhance our ability to both analyze and manipulateglycoprotein structure and function.

Methods were previously developed which for the first time allowed thesystematic addition of amino acids with novel chemical and physicalproperties to the genetic code of E. coli (see, e.g., L. Wang, et al.,(2001) Science 292:498; L. Wang, et al., (2002) J. Am. Chem. Soc.124:1836; Z. Zhang, et al., (2002) Angew. Chem. Int. Ed. Engl. 41:2840;J. W. Chin et al., (2002) J. Am. Chem. Soc. 124:9026; J. W. Chin et al.,(2002) Proc. Natl. Acad. Sci. USA 99:11020; S. W. Santoro, et al.,(2002) Nat. Biotechnol. 20:1044; L. Wang, et al., (2003), Proc. Natl.Acad. Sci. USA 100:56; and, Z. Zhang et al., (2003) Biochemistry42:6735) and yeast (see, e.g., J. W. Chin et al., Science, (2003 inpress). In this approach, an amber suppressor M. jannaschiiTyr  RS − mu  tRNA_(CUA)^(Tyr)pair that does not cross-react with endogenous tRNAs and synthetases isevolved to uniquely charge a desired unnatural amino acid. Thismethology can also allow one to directly incorporate glycosylated,phosphorylated, or methylated amino acids into proteins (see, e.g., T.Arslan, et al., (1997) J. Am. Chem. Soc. 119:10877), avoiding the needfor selective enzymatic or chemical posttranslational modification ofproteins. B-O-GlcNAc-L-serine (Compound A, GlcNAc: N-acetylglucosamine)was attempted to be site-specifically incorporated into proteins in E.coli. The O-GlcNAc modification is ubiquitous in nearly all eukaryotes,is involved in regulation of cell signaling, protein trafficking andcell growth, and is also a substrate from which more complexcarbohydrates are generated. See, e.g., L. Wells, et al., (2001) Science291:2376; and, N. Lamarre-Vincent, & L. Hsieh-Wilson, (2003) J. Am.Chem. Soc. 125:6612. Unfortunately, saccharide derivatives with freehydroxyl groups are transferred poorly across the membrane of eukaryoticcells, suggesting that substrate Compound A would unlikely becell-permeable. See, e.g., A. K. Sarkar, et al., (1995), Proc. Natl.Acad. Sci. USA 92:3323. However, it has been shown that acetylation ofthe hydroxyl groups of sugars facilitates transport across cellmembranes and that the hydroxyl acetyl groups can be deacetylated bynonspecific cytosolic esterases once inside the cell. See, e.g., N.Lamarre-Vincent, & L. Hsieh-Wilson, (2003) J. Am. Chem. Soc. 125:6612.Therefore, the acetylated derivative tri-acetyl-β-GlcNAc-serine CompoundB, for which there is a commercially available precursor,N-Fmoc-tri-acetyl-β-GlcNAc-serine, was used in these experiments.Compound:

A series of positive and negative selections was used to isolate from alibrary of active site mutants, a TyrRS that specifically charges theorthogonal mu  tRNA_(CUA)^(Tyr)with β-GlcNAc-serine in E. coli. Based on the X-ray structure of thehomologous Bacillus stearothermophilus TyrRS, two libraries wereconstructed with active site residues randomized: one, encoded byplasmid pBK-lib-m, had residues Tyr³², Ala⁶⁷, His⁷⁰, Gln¹⁵⁵, Asp¹⁵⁸, andAla¹⁶⁷ randomized, and a second, encoded by plasmid pBK-lib, hadresidues Tyr³², Glu¹⁰⁷, Asp¹⁵⁸, Ile¹⁵⁹, and Leu¹⁶² randomized. Theseresidues are all within 6.9 Å of the phenyl ring and are the primaryresidues that form the substrate binding pocket. The combined libraryhad approximately 2.6×10⁹ independent clones. This library was thensubjected to a positive selection, based on suppression of an ambercodon introduced at Asp112 in the chloramphenicol acetyltransferase(CAT) gene, to select TyrRS mutants capable of incorporating theglycosylated amino acid. Cells surviving at high concentrations ofchloramphenicol must express a mutant TyrRS with the ability to inserteither β-GlcNAc-serine or an endogenous amino acid in response to theAsp112TAG amber codon. A negative selection, based on suppression ofthree amber codons in the toxic barnase gene, was then used to deletefrom the selected clones those mutant TyrRSs that incorporate endogenousamino acids. After five rounds of positive selection and four rounds ofnegative selection, three clones emerged which survived at highconcentration of chloramphenicol. These clones and their mutations areas following: S1-90 (Glu¹⁰⁷→Pro¹⁰⁷, Asp¹⁵⁸→Cys¹⁵⁸, Ile¹⁵⁹→Tyr¹⁵⁹,Leu¹⁶²→Arg¹⁶²), S4-5 (Tyr³² Gly³², Glu¹⁰⁷→Gly¹⁰⁷, Asp¹⁵⁸→Cys¹⁵⁸,Leu¹⁶²→His¹⁶²), S1-5 (Glu¹⁰⁷→Cys¹⁰⁷, Asp¹⁵⁸→His¹⁵⁸, Ile¹⁵⁹→Asp¹⁵⁹,Leu¹⁶²→Met¹⁶²). All of these clones appear to be highly selective forβ-GlcNAc-serine, since replacement of Compound B with 1 mM of serine,α-tri-acetyl-GalNAc-threonine, α/β-tri-acetyl-GalNAc-serine orβ-tetra-acetyl-Glu-asparagine does not permit cell growth above 30 μg/mlof chloramphenicol. These in vivo genetic results suggest that the newlyselected mutant TyrRSs have excellent specificity towardsβ-GlcNAc-L-serine.

To test the efficiency and fidelity of incorporation of Compound B, amutant myoglobin gene (Gly4TAG) containing an amber codon at the fourthposition and a C terminal His6 tag was generated. See, e.g., S. W.Santoro et al., (2002) Nat. Biotechnol. 20:1044. When the mutantsynthetase, S1-90, was co-expressed with the mu tRNA_(CUA) ^(Tyr) andGly4TAG myoglobin genes in the presence of Compound B in minimal media,1 mg/L of the full length mutant myoglobin was produced (See FIG. 4).For comparison, 5.5 mg/L of wild-type myoglobin was produced undersimilar condition, indicating a good level of suppression for S1-90. Inthe absence of either S1-90, mu  tRNA_(CUA)^(Tyr),or Compound B, no expression of full-length myoglobin was observed bysilver-stained SDS-PAGE (See FIG. 4).

FIG. 4 illustrates expression of the Gly4→Compound A mutant myoglobin(˜18.5 kD). Proteins were purified by Ni²⁺-affinity chromatography andresolved by SDS-PAGE. The gel was silver-stained. Lane 1 shows myoglobinwas expressed in the presence of the orthogonal tRNA, synthetase S1-90,and Compound B. The band at ˜18 kDa corresponds to the full-lengthmyoglobin. Lane 2 shows proteins eluted after expression in the presenceof the orthogonal tRNA and the synthetase S1-90 but in the absence ofsubstrate Compound B. Lane 3 shows proteins eluted after expression inthe presence of the orthogonal tRNA and substrate Compound B but in theabsence of synthetase S1-90. Lane 4 shows proteins eluted afterexpression in the presence of the synthetase S1-90 and substrateCompound B but in the absence of the orthogonal tRNA. Lane 5 containsthe purified wild type myglobin for comparison.

High resolution MALDI-TOF analysis afforded a monoisotopic mass of theHis6 tag-purified mutant myoglobin of 18430.1 Da, which agrees within 32ppm with the theoretical mass of myoglobin containing Glc(OH)₃Nac-serinewithout methionine (M_(theoretical)=18429.5 Da). See FIG. 5. Note thatthe loss of the N terminal Met is common in E. coli. In addition, nosignals corresponding to either the O-acetylated glycomyoglobin or thewild-type myoglobin were observed. The mass spectrum data confirm a highdegree of specificity for the incorporation of GlcNAc-serine intomyoglobin (≧96%).

Several additional experiments were performed to further characterizethe mutant myoglobin. First, an ELISA-like assay was used to analyze thebinding of a GlcNAc-specific lectin, Bandeiraea simplicifolia II (BSII)(see, e.g., S. Ebisu, et al., (1978), Carbohydr. Res. 61:129), towild-type myoglobin and glyco-myoglobin. See FIG. 6, Panel A. FIG. 6,Panel A illustrates binding of a GlcNAc-specific lectin, Banderiraeasimplicifolia II (BSII), to wild-type myoglobin and glycomyoglobin. A₄₀₅values are shown for wild-type myoglobin, glycomyoglobin, and negativecontrol (no lectin added). Gly4→Compound A mutant myoglobin (200 ng) andwild type myoglobin (200 ng) were immobilized in microtiter plate wellsand subsequently incubated with biotinylated BSII andstreptavidin-alkaline phosphatase conjugate. Wells were incubated withp-nitrophenyl phosphate and monitored by measuring the absorbance at 405nm. The two forms of myoglobin were immobilized in microtiter platewells and then incubated with biotinylated BSII, streptavidin-alkalinephosphatase conjugate, and p-nitrophenyl phosphate, respectively. Wellscontaining wild-type myoglobin afforded a signal equivalent to negativecontrol wells. In contrast, wells containing glycomyoglobin produced asignal at least 200 fold higher than that of wild-type myoglobin,demonstrating selective recognition by the GlcNAc-specific lectin. Inaddition, this result shows that the carbohydrate has not been modifiedto other isomeric forms such as GalNAc and ManNAc since this lectin ishighly selective for GlcNAc (see, e.g., S. Ebisu, et al., (1978),Carbohydr. Res. 61:129).

We also investigated whether the O-GlcNAc-serine residue in myoglobincould be selectively modified with a galactosyltransferase.Beta-1,4-galactosyltransferase is known to transfer galactose (Gal) fromthe sugar nucleotide UDP-Gal to the 4 position of an N-acetylglucosamine(GlcNAc) to form Galβ1,4GlcNAc. To determine if the O-glycosylatedmyoglobin can be modified with UDP-Gal, both wild-type andO-glycosylated myoglobin were resolved by SDS-PAGE and transferred to aPVD membrane. The membrane was then incubated with bovin milkgalactosyltransferase and radioactive UDP-[H³]-galactose at roomtemperature for 24 hours. See, e.g., K. Kamemura, et al., (2002), J.Biol. Chem. 277:19229. Incorporation of [H³]-Gal was monitored byexposing the membrane to X-ray film. Only the glycomyoglobin waslabeled; no detectable signal was observed for the wild-type myoglobin.See FIG. 6, Panel B. FIG. 6, Panel B illustrates on-blotgalactosyltransferase labeling glycomyoglobin with UDP-[H³]galactose.Wild type myoglobin (1 μg) and Gly4→Compound A mutant myoglobin (1 μg)were resolved by 12% SDS-PAGE and transferred to a PVD membrane. Themembrane was then treated with bovine milk galactosyltransferase (1 U),UDP-[H³]galactose (0.5 μCi) and calf intestinal alkaline phosphatase (1U) for 24 hours at room temperature. After extensive washes, themembrane was exposed to X-ray film using Enhanced autoradiography.

For quantitative analysis, the glycosyltransfer reaction was alsocarried out in solution. See, e.g., K. Witte, et al., (1997) J. Am.Chem. Soc. 119:2114. After incubation for 48 hours at room temperature,a 72% yield of disaccharide was obtained based on the radiolabelpresent. See FIG. 6, Panel C. FIG. 6, Panel C illustrates quantitativeanalysis of the galactosyltransferase reaction, which was carried out insolution, and the radiolabeled galactose was normalized such that 1.0corresponds to 100% transfer. To the solutions containing HPLC-purifiedwild type myoglobin (100 μg) and Gly4 Compound A mutant myoglobin (100μg) were added pyruvate kinase (5 U), UDP-glucose pyrophosphorylase (1U), inorganic pyrophosphorylase (10 U), galactose-1-phosphate-uridyltransferase (1 U), bovine milk galactosyltransferase (2 U),glucose-1-phosphate (3 μmol), uridyl diphosphate (3 μmol),phosphoenolpyruvate (0.01 mmol), and DTT (2 μmol). After the reactionwas adjusted to pH 7.2, [H³]-galactose-1-phosphate (0.01 mmol) wasadded. The reaction was carried out for 48 hours at room temperature.Protein products were separated with a PD-10 Sephadex 25 column.Incorporated radiolabel was measured on a liquid scintillation analyzer.

These studies demonstrate that β-GlcNAc-L-serine can becotranslationally incorporated into proteins in E. coli with excellentspecificity and good yield. The incorporated β-GlcNAc-serine can serveas a primary glycosylation site to which saccharides can be addedsequentially with glycosyltransferase, e.g., K. Kamemura, et al.,(2002), J. Biol. Chem. 277:19229.

Materials and Methods

Directed evolution of mutant TyrRS enzymes. The general procedures forthe positive and negative selections have been reported previously. See,e.g., Z. Zhang et al., (2003) Biochemistry, 42:6735. Briefly, acombination of plasmid pBK-lib-m (see, e.g., Z. Zhang et al., (2003)Biochemistry 42:6735) and pBK-lib (see, e.g., L. Wang, et al., (2001)Science 292:498) was transformed into competent E. coli DH10B harboringthe plasmid pRep(2)/YC (see, e.g., S. W. Santoro, et al., (2002) Nat.Biotechnol. 20:1044). The transformed cells were grown in 500 ml of GMMLmedium (1×M9 minimal media with 1% glycerol, 0.3 mM leucine, 1 mM MgCl₂,0.1 mM CaCl₂ and 0.5% NaCl) containing 40 μg/ml tetracycline, 50 μg/mlkanamycin, 68 μg/ml chloramphenicol, and 1 mM Compound B for 60 hours at37° C. Plasmids (pBK) were purified from surviving cells and transformedinto E. coli DH10B harboring pLWJ17B3 (see, e.g., L. Wang, et al.,(2001) Science 292:498) to start the negative selection. Cells were thenplated onto LB (Luria-Bertani) plates containing 40 μg/mlchloramphenicol, 50 μg/ml kanamycin, and 0.02% L-arabinose and incubatedat 37° C. for 8 hours. Plasmids pBK were purified from surviving cellsand used for the subsequent positive and negative selections. After fiverounds of positive and four rounds of negative selections, threecandidate pairs of orthogonal tRNA-synthetases that conferredsubstrate-dependent chloramphenicol resistance were isolated andsequenced.

Expression and characterization of mutant myoglobin. DH10B cellscontaining pBAD/JYAMB4TAG (see, e.g., S. W. Santoro, et al., (2002) Nat.Biotechnol. 20:1044) and pS1-90 were grown in a 500 ml GMML culturecontaining kanamycin, tetracycline, 0.02% L-arabinose, 5 μM FeCl₃, and 0or 1 mM of Compound B. The cells were pelleted, lysed, and the proteinswere purified by affinity chromatography with Ni²⁺-NTA beads undernative conditions. Proteins were analyzed by 12% SDS-PAGE andsilver-stained. Aliquots of purified proteins were subject to highresolution mass spectrometric analysis. Matrix-assisted laser desorptionionization (MALDI) with a time-of-flight (TOF) mass spectrometer(Voyager DE-STR, Applied Biosystems, Foster City, Calif.) was used tomeasure the molecular weight of the protein. Protein samples weredesorbed and ionized upon irradiation from a 337 nm nitrogen laser.Sinapinic acid was used as the MALDI matrix. Lectin binding andglycosyltransferase reactions were carried out following the establishedprotocols (see, e.g., K. Kamemura, et al., (2002), J. Biol. Chem.277:19229; and, K. Witte, et al., (1997) J. Am. Chem. Soc. 119:2114).

Example 5 Sequences of Exemplary O-RSs

Exemplary O-RSs that can be used in the invention include SEQ ID Nos:1-6 (See Table 2), and exemplary O-tRNA that can be used in theinvention includes SEQ ID NO: 7. Exemplary polynucleotides that encodeO-RSs include SEQ ID NOs.: 8-10.

It is understood that the examples and embodiments described herein arefor illustrative purposes only and that various modifications or changesin light thereof will be suggested to persons skilled in the art and areto be included within the spirit and purview of this application andscope of the appended claims.

While the foregoing invention has been described in some detail forpurposes of clarity and understanding, it will be clear to one skilledin the art from a reading of this disclosure that various changes inform and detail can be made without departing from the true scope of theinvention. For example, all the techniques and apparatus described abovecan be used in various combinations. All publications, patents, patentapplications, and/or other documents cited in this application areincorporated by reference in their entirety for all purposes to the sameextent as if each individual publication, patent, patent application,and/or other document were individually indicated to be incorporated byreference for all purposes. TABLE 2 EXAMPLES OF SEQUENCES SEQ ID #Sequences Notes RS 1 MDEFEMIKRNTSEIISEEELREVLKKDEKSALIGFEPSGKI LW1RS RSHLGHYLQIKKMIDLQNAGFDIIILLADLHAYLNQKGELDEI aaRKIGDYNKKVFEAMGLKAKYVYGSEFQLDKDYTLNVYRLALKTTLKRARRSMELIAREDENPKVAEVIYPIMQVNGCHYRGVDVAVGGMEQRKIHMLARELLPKKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEIRAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPEKFGGDLTVNSYEELESLFKNKELHPMDL KNAVAEELIKILEPIRKRL 2MDEFEMIKRNTSEIISEEELREVLKKDEKSALIGFEPSGKI LW5RS RSHLGHYLQIKKMIDLQNAGFDIIILLADLHAYLNQKGELDEI AARKIGDYNKKVFEAMGLKAKYVYGSEFQLDKDYTLNVYRLALKTTLKRARRSMELIAREDENPKVAEVIYPIMQVNGGHYLGVDVAVGGMEQRKIHMLARELLPKKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEIRAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPEKFGGDLTVNSYEELESLFKNKELHPMDL KNAVAEELIKILEPIRKRL 3NDEFEMIKRNTSEIISEEELREVLKKDEKSAAIGFEPSGKI LW6RS RSHLGHYLQIKKMIDLQNAGFDIIILLADLHAYLNQKGELDEI aaRKIGDYNKKVFEAMGLKAKYVYGSEFQLDKDYTLNVYRLALKTTLKRARRSNELIAREDENPKVAEVIYPIMQVNGGHYLGVDVIVGGMEQRKIHMLARELLPKKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEIRAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPEKFGGDLTVNSYEELESLFKNKELHPMDL KNAVAEELIKILEPIRKRL 4MDEFENIKRNTSEIISEEELREVLKKDEKSAYIGFEPSGKI S1-90 RSHLGHYLQIKKMIDLQNAGFDIIILLADLHAYLNQKGELDEI aaRKIGDYNKKVFEAMGLKAKYVYGSPFQLDKDYTLNVYRLALKTTLKRARRSMELIAREDENPKVAEVIYPIMQVNCYHYRGVDVAVGGNEQRKIHMLARELLPKKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEIRAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPEKFGGDLTVNSYEELESLFKNKELHPMDL KNAVAEELIKILEPIRKRL 5MDEFEMIKRNTSEIISEEELREVLKKDEKSAGIGFEPSGKI S4-5 RSHLGHYLQIKKMIDLQNAGFDIIILLADLHAYLNQKGELDEI aaRKIGDYNKKVFEAMGLKAKYVYGSGFQLDKDYTLNVYRLALKTTLKRARRSMELIAREDENPKVAEVIYPIMQVNCMHYHGVDVAVGGMEQRKIHMLARELLPKKVVCIHNPVLTGLDGEGKMSSSKGNFIAVDDSPEEIRAKIKKAYCPAGVVEGNPIMEIAKYFLEYPLTIKRPEKFGGDLTVNSYEELESLFKNKELHPMDL KNAVAEELIKILEPIRKRL 6MDEFENIKBNTSEIISEEELREVLKKDEKSAYIGFEPSGKI S1-5 RSHLGHYLQIKKMIDLQNAGFDIIILLADLHAYLNQKGELDEI aaRKIGDYNKKVFEAMGLKAKYVYGS[C/S]FQLDKDYTLNVY PositionRLALKTTLKRARRSMELIAREDENPKVAEVIYPIMQVNHDH 107 can beYMGVDVAVGGMEQRKIHMLARELLPKKVVCIHNPVLTGLDG either aEGKMSSSKGNFIAVDDSPEEIRAKIKKAYCPAGVVEGNPIM C or SEIARYFLEYPLTIKRPEKFGGDLTVNSYEELESLFKNKELH PMDLKNAVAEELIKILEPIRKRL 7CCGGCGGUAGUUCAGCAGGGCAGAACGGCGGACUCUAAAUC mutRNA_(CUA) ^(Tyr) tRNACGCAUGGCGCUGGUUCAAAUCCGGCCCGCCGGACCA 8ATGGACGAATTTGAAATGATAAAGAGAAACACATCTGAAAT S1-90 RSTATCAGCGAGGAAGAGTTAAGAGAGGTTTTAAAAAAAGATG polynu-AAAAATCTGCTTACATAGGTTTTGAACCAAGTGGTAAAATA cleotideCATTTAGGGCATTATCTCCAAATAAAAAAGATGATTGATTTACAAAATGCTGGATTTGATATAATTATATTGTTGGCTGATTTACACGCCTATTTAAACCAGAAAGGAGAGTTGGATGAGATTAGAAAAATAGGAGATTATAACAAAAAAGTTTTTGAAGCAATGGGGTTAAAGGCAAAATATGTTTATGGAAGTCCATTCCAGCTTGATAAGGATTATACACTGAATGTCTATAGATTGGCTTTAAAAACTACCTTAAAAAGAGCAAGAAGGAGTATGGAACTTATAGCAAGAGAGGATGAAAATCCAAAGGTTGCTGAAGTTATCTATCCAATAATGCAGGTTAATTGCTATCATTATAGGGGCGTTGATGTTGCAGTTGGAGGGATGGAGCAGAGAAAAATACACATGTTAGCAAGGGAGCTTTTACCAAAAAAGGTTGTTTGTATTCACAACCCTGTCTTAACGGGTTTGGATGGAGAAGGAAAGATGAGTTCTTCAAAAGGGAATTTTATAGCTGTTGATGACTCTCCAGAAGAGATTAGGGCTAAGATAAAGAAAGCATACTGCCCAGCTGGAGTTGTTGAAGGAAATCCAATAATGGAGATAGCTAAATACTTCCTTGAATATCCTTTAACCATAAAAAGGCCAGAAAAATTTGGTGGAGATTTGACAGTTAATAGCTATGAGGAGTTAGAGAGTTTATTTAAAAATAAGGAATTGCATCCAATGGATTTAAAAAATGCTGTAGCTGAAGAACTTATAAAGATTTTAGAGCC AATTAGAAAGAGATTATAA 9ATGGACGAATTTGAAATGATAAAGAGAAACACATCTGAAAT S4-5 RSTATCAGCGAGGAAGAGTTAAGAGAGGTTTTAAAAAAAGATG polynu-AALAATCTGCTGGAATAGGTTTTGAACCAAGTGGTAAAATA cleotideCATTTAGGGCATTATCTCCAAATAAAAAAGATGATTGATTTACAAAATGCTGGATTTGATATAATTATATTGTTGGCTGATTTACACGCCTATTTAAACCAGAAAGGAGAGTTGGATGAGATTAGAAAAATAGGAGATTATAACAAAAAAGTTTTTGAAGCAATGGGGTTAAAGGCAAAATATGTTTATGGAAGTGGATTCCAGCTTGATAAGGATTATACACTGAATGTCTATAGATTGGCTTTAAAAACTACCTTAAAAAGAGCAAGAAGGAGTATGGAACTTATAGCAAGAGAGGATGAAAATCCAAAGGTTGCTGAAGTTATCTATCCAATAATGCAGGTTAATTGTATGCATTATCACGGCGTTGATGTTGCAGTTGGAGGGATGGAGCAGAGAAAAATACACATGTTAGCAAGGGAGCTTTTACCAAAAAAGGTTGTTTGTATTCACAACCCTGTCTTAACGGGTTTGGATGGAGAAGGAAAGATGAGTTCTTCAAAAGGGAATTTTATAGCTGTTGATGACTCTCCAGAAGAGATTAGGGCTAAGATAAAGAAAGCATACTGCCCAGCTGGAGTTGTTGAAGGAAATCCAATAATGGAGATAGCTAAATACTTCCTTGAATATCCTTTAACCATAAAAAGGCCACAAAAATTTGGTCGAGATTTGACAGTTAATAGCTATGAGGAGTTAGAGAGTTTATTTAAAAATAAGGAATTGCATCCAATGGATTTAAAAAATGCTGTAGCTGAAGAACTTATAAAGATTTTAGAGCC AATTAGAAAGAGATTATAA 10ATGGACGAATTTGAAATGATAAAGAGAAACACATCTGAAAT S1-5 RSTATCAGCGAGGAAGAGTTAAGAGAGGTTTTAAAAAAAGATG polynu-AAAAATCTGCTTACATAGGTTTTGAACCAAGTGGTAAAATA cleotideCATTTAGGGCATTATCTCCAAATAAAAAAGATGATTGATTTACAAAATGCTGGATTTGATATAATTATATTGTTGGCTGATTTACACGCCTATTTAAACCAGAAAGGAGAGTTGGATGAGATTAGAAAAATAGGAGATTATAACAAAAAAGTTTTTGAAGCAATGGGGTTAAAGGCAAAATATGTTTATGGAAGTTCATTCCAGCTTGATAAGGATTATACACTGAATGTCTATAGATTGGCTTTAAAAACTACCTTAAAAAGAGCAAGAAGGAGTATGGAACTTATAGCAAGAGAGGATGAAAATCCAAAGGTTGCTGAAGTTATCTATCCAATAATGCAGGTTAATCATGATCATTATATGGGCGTTGATGTTGCAGTTGGAGGGATGGAGCAGAGAAAAATACACATGTTAGCAAGGGAGCTTTTACCAAAAAAGGTTGTTTGTATTCACAACCCTGTCTTAACGGGTTTGGATGGAGAAGGAAAGATGAGTTCTTCAAAAGGGAATTTTATAGCTGTTGATGACTCTCCAGAAGAGATTAGGGCTAAGATAAAGAAAGCATACTGCCCAGCTGGAGTTGTTGAAGGAAATCCAATAATGGAGATAGCTAAATACTTCCTTGAATATCCTTTAACCATAAAAAGGCCAGAAAAATTTGGTGGAGATTTGACAGTTAATAGCTATGAGGAGTTAGAGAGTTTATTTAAAAATAAGGAATTGCATCCAATGGATTTAAAAAATGCTGTAGCTGAAGAACTTATAAAGATTTTAGAGCC AATTAGAAAGAGATTATAA

1-34. (canceled)
 35. A method for synthesis of a glycoprotein, the method comprising incorporating into a protein an unnatural amino acid that comprises a saccharide moiety.
 36. The method of claim 35, wherein the method further comprises contacting the saccharide moiety with a glycosyltransferase, a sugar donor moiety, and other reactants required for glycosyltransferase activity for a sufficient time and under appropriate conditions to transfer a sugar from the sugar donor moiety to the saccharide moiety.
 37. The method of claim 36, wherein the glycosyltransferase is selected from the group consisting of: a galactosyltransferase, a fucosyltransferase, a glucosyltransferase, an N-acetylgalactosaminyltransferase, an N-acetylglucosaminyltransferase, a glucuronyltransferase, a sialyltransferase, a mannosyltransferase, a glucuronic acid transferase, a galacturonic acid transferase, and an oligosaccharyltransferase.
 38. The method of claim 36, wherein the method further comprises contacting the product of the glycosyltransferase reaction with at least a second glycosyltransferase and a second sugar donor moiety.
 39. The method of claim 36, wherein the saccharide moiety comprises a terminal GlcNAc, the sugar donor moiety is UDP-GlcNAc and the glycosyltransferase is a β1-4N-acetylglucosaminyltransferase.
 40. The method of claim 36, wherein the saccharide moiety comprises a terminal GlcNAc, the sugar donor moiety is UDP-Gal and the glycosyltransferase is a β1-4-galactosyltransferase.
 41. The method of claim 35, wherein the incorporating step comprises using an orthogonal tRNA/orthogonal aminoacyl-tRNA synthetase (O-tRNA/O-RS) pair, wherein the O-tRNA recognizes a selector codon and incorporates the unnatural amino acid into the protein in response to the selector codon, and wherein the O-RS preferentially aminoacylates the O-tRNA with the unnatural amino acid.
 42. The method of claim 41, wherein the O-RS comprises an amino acid sequence comprising any one of SEQ ID NO.: 4, 5 or
 6. 43. The method of claim 41, wherein the O-tRNA comprises a mutRNA_(CUA)^(Tyr).
 44. The method of claim 35, wherein the incorporating step is in vivo.
 45. The method of claim 35, wherein the unnatural amino acid comprises a β-O-GlcNAc-L-serine, a tri-acetyl-β-GlcNAc-serine, a tri-O-acetyl-GalNAc-α-threonine, or an α-GalNAc-L-threonine. 46-57. (canceled) 